On the character of judgments in the moral domain
Here, I do want to provide some guidance, based on my various reading and reflection for several years now. I'm going to be very schematic, but it's important.
Speculative vs. Practical
There are some you will read (McInerny is classic here, though see some of things that C. Cuddy cites) who seem to hold that everything short of the command of prudence is speculative in nature. There are perhaps a few texts in Aquinas that lead one to think this, but there are many others that lead away from it. The School was conflicted here too (as can be witnessed for example in John of St. Thomas). However, based on a kind of synthesis of various streams, I will be presenting what I take to be the sanest way to read these matters. It is based on a great devotion to this topic, and while I'm no "scholar" of them in the sense of having done a full "lit review," I personally have found it very helpful in my teaching. My view is a combination, though admittedly unique, of the strand one finds in Gardeil, Maritain, Garrigou, Merkelbach, Simon, and Labourdette.
Point 1: The entire domain of moral truth is distinct from merely speculative truths
The truths of practico-moral (as contrasted to practical-artistic/technical) are destined to be forms of operabilia. They have their foundation on ontology, but it is a separate domain. All
Point 2: The root source of moral reflection is (a) in the natural order, synderesis; (b) in the supernatural order, faith perhaps filtered through superelevated synderesis, used instrumentally by faith (see Merkelbach on this)
Even in the natural order, I hold (with others of no small weight) that synderesis is a habitus of principles distinct from intellectus as ordered to purely speculative truths (e.g., the first principles of natural philosophy or of metaphysics). It presupposes intellectus (as well as the whole domain of speculative knowledge in its various forms as opinions, observations, and sciences). Faith certainly is separate. Both syndersis and faith, however, are direct, non-objectively-illative knowledge of principles.
Point 3: Paths immediately diverge at this point. This is an important juncture point. One can either go down the path of (a) what we will call, following the tradition, though not without its problems, "moral science" (i.e., moral philosophy or moral theology) or (b) personal action, considered proximately or distantly.
This is a very important distinction. In "moral science" we do indeed study how the various principles of acts are dependent on each other (the end, habitus, virtues / vices, law, the various virtues in particulari, etc.). However, we also have to form "case studies" which are still somewhat generalized. Such casuistic judgments are a moral-scientific attempt to come up with general rules concerning potential human actions. These technically should be handled in relation to each particular virtue (Gardeil-Beaudouin make this point; also, see Brian Besong's article in the ACPQ concerning the manualist tradition and casuistry; I don't agree 100% with him, but he's quite right on a lot). However, at this level of reflection, we are considering a kind of X to whom a given action might apply. We are not engaging the subject in his or her relationship to his or her own action. People like McInerny McInerny and Cuddy (maybe Labourdette too? I'm not sure right now) think that conscience is this kind of judgment. However, it is very difficult for me to square this with how Aquinas talks about conscience at times: condemning one's own action, etc. (e.g., ST I, q. 79, a. 13: "....For conscience is said to witness, to bind, or incite, and also to accuse, torment, or rebuke.") My opinion is that historically Aquinas was not situated at a point where all of these distinctions could be made. But, in this case, following the later Thomists, we would call this judgment NOT speculative BUT RATHER speculatively-practical.
Point 4: One can even speculatively practically reflect upon one's own activity.
Think, for example of consequent conscience when we consider what we did in the past. This has less engagement of the will than will be had in what follows. We will only, however, here be concerned with antecedent conscience.
Point 5: I think the distinction between conscience and moral reasoning hic et nunc is in important distinction; however, we must be careful not to disconnect "moral science" from moral character
Here, I think that the Thomist school has been too ready to say, "You can be a good moral philosopher but a bad person." I think that the very nature of moral truth is such that even reflection on it is intrinsically tied to the possibility of doing moral philosophy (let alone theology). There are some basic things you can know because, indeed, synderesis is forever the light that can at least grasp basic truths. Look, however, at how whole people create perverse moral theologies / philosophies all because of their own character. (Alas, the person who came to my mind is the tragic case of Dr. Mark Jordan in his advocacy for his homosexual lifestyle, which now creeps into everything he does. And, the more I have heard about him personally, I find him all the more tragic. Let us pray for him.) In any case, think of how casuistry is highly dependent upon one's moral character. Whence, if the judgment of conscience is something akin to "moral science," it is nonetheless requires no small character formation. (And, to the degree that empirical data are needed for moral science, character matters immensely.) This is all why Aristotle said the things he did in books 1 and 2 of the Nicomachaean Ethics, and it has been under-appreciated by many Thomists in my opinion. Character intrinsically matters in moral philosophy as an intrinsic condition for it to exist in statu scientiae (and not merely as a kind of ensemble of quasi-scientific truths without scientific unity). It would take a kind of demonic malice to see these truths, set them forth, and yet spurn them. Humanly speaking, some (but not total) character seems to be required here—and let us remember that the sciences are human affairs, not abstract Platonized bodies of ideas floating around in the heavens.
Point 6: Okay, let's move quickly. Remember about prudence: (a) it presupposes the order of intention; without this, it has no end or ultimate rectification through the various virtues; (b) it is related to virtues differently (there is a medium rationis for temperance / courage; there is a medium rei for matter of justice - though this needs more discussion among Thomists, I think; and the case of the theological virtues is quite unique, given their lofty formal objects); (c) it has BOTH judgment / choice and command as part of its procedure. Here, you must WHOLLY ignore Dom Lottin, as well as anyone who talks only about judgment and choice while forgetting command. (Leonard Lehu is guilty of this in his own way, too, I think.)
Point 7: Moral judgments in the order of intention
There are moral judgments in the order of intention. Here, note that we are already talking about an agent who is considering whether this good also should be my own good. In other words, we have shifted from mere "moral science" to something more subjective and hence dependent much more heavily upon rectification of appetite. Thus, synderesis and "moral science" judges concerning certain virtues and we have "simple willing", which is as profound as Gardeil and Pinckaers both see it to be. Here, the will rests in the good as something that I truly love (even if it's not something to be done here and now). I refer here to 1 and 2 on the famous 16 step chart.
There also is a judgment of intention which will rule the will's intention. It is reciprocally related to the intention of the end. Here, we have passed from mere consideration of what it is we might do to what we must do. Without inchoate virtue (or, at the very beginning of moral formation, the basic orientation of the will to its own, proper good) prudence cannot do its task. (This is 3 and 4 on the famed chart.)
Point 8: Moral judgments in the order of election / choice
In the "order of choice" we have an immense field of tasks. You should read in my Gardeil volume the whole lengthy chapter on self-governance. It is the best summary of prudence I have ever encountered, far better than the superficial presentations usually given for it.
Here, there are judgments of counsel, requiring various virtues in order to be right. Here, we come up with various possible judgments that may well be fitting for me here and now. Certain scholastics would speak of these as being judgments about the means in globo. There is an intrinsic dependence upon the various virtues related to prudence. One must never think of the intellectual and volitional parts of this chart as being completely dissociated. They mutually condition each other, as Fr. Garrigou—following the school— shows well. Way too many Thomists treat all of this as being merely intellectual. And in doing this, I assure you, they cheapen moral reasoning, do away with prudence as a virtue, and give way to scoffing by Pope Francis and his like. Again, read Gardeil to see what all I mean. In any case, this is a very personalized judgment. I personally hold that this cannot be just a consideration of "just any old X" who may do this action. I am taking counsel (with myself and others) concerning an act that I intend to do. This represents one more stage in the continued existential self-appropriation of the good of the end. (This is 5 and 6 of the famed chart.)
But, even with all of this, we need to come to the unity of the practical judgment—and here often great virtue is needed; whence, the great virtues of synesis and gnome. Here, you'll see the position of a Garrigou or a Merkelbach, who said that right and certain conscience is actually found in this judgment. Perhaps they are wrong (I lean in the direction of thinking that they are), and yet they are inspired by this very important insight: judgments of conscience are about acts, which may well become incorporated into prudential reasoning so as to become MY act. On the interrelation between the terminal judgment of prudence and the act of will required—i.e., how choice and judgment have mutual causality on each other, one in the order of exercise and the other in the order of formal causality—you must see Garrigou (esp. in vol. 2 of God: His existence and His nature). This is something so important in these matters. Here, in any case, the judgments in question are highly personalized, to the point that they ultimately become almost incommunicable. Command will be fully incommunicable. (Anyway, here, we have 7 and 8 on the famed chart.)
Point 9: The order of command
It is precisely because command remains (which is the perfection of prudence) that people like RGL and Merkelbach thought they could incorporate right and sure conscience into prudence. Yet, here, we pass out from the domain of choice, though and hence beyond conscience. Note, if you so desire, the particular way that the virtues named foresight, circumspection, and precaution have particular roles to play here in the order of command. Gardeil notes this well. Command is incommunicable precisely because it is the practical intellect informing the will in its action. It is only known communicably by way of reflection. (Whence, there is such opacity involved in examining our past actions—they were never this clear.)