[This seems like a rather bold task, but some consideration of we come to know is essential if we're going to make sense of the difficulties involved in knowing matter and if we are to give an account of how God knows at all. I think I have the truths about these things in my mind, but I'm not at all comfortable determining the order of approach. Nor is it clear to what extent these things should be considered.]
All human knowledge begins with the senses. Sensation occurs when a sense organ is acted upon by a sensible object in such a way that the sensible form is received in a way other than the way matter receives forms. For example, a rock can be heated but cannot feel heat; on the other hand, if a man stands near a fire, he will not only become heated, but he will feel the heat. This cognition or awareness of heat is peculiar to sensation, and requires a possibility to receive which goes beyond the capacity of non-living bodies. Furthermore, our senses can be brought into act only by some sensible object acting on it, which requires that it actually have some sensible quality. Since prime matter is pure potency, as was said above, (and potency is opposed to actuality) prime matter will be incapable of acting upon our senses in virtue of itself.
Beyond the senses, man also has a mind or intellect. By this power he is able to abstract from what his senses receive and know things in a universal way. For example, man not only sees this red and that red, but has abstracted from this sense experience a universal concept of red, through which he is able think about and make statements about red, without attending to some particular instance of it (e.g. red is my favorite color, apples are red, and so on). It is not by our intellect abstracting that we have a concept of prime matter. Since abstraction only happens by making universal what is perceived by the senses, and prime matter is not an object of sensation, prime matter is not abstracted from our senses. Our concept of it comes from an argument (like the one given above) and depends on other concepts which we have abstracted from our senses. So when it is said that prime matter is pure potency to substance, we understand this through an analogy of how a substance stands to its accidents, substance and accident being two concepts which we have abstracted from sensation. (a footnote or perhaps some more body where I mention the truth that "everything is intelligible insofar as it is act")
Although we are able to form some analogous concept of prime matter, we only understand it by likening it to something else which is actual. Prime matter in itself still seems to remain unknown and even unknowable. Now it remains a question as to whether God knows prime matter in itself. Before this, we must first consider God's knowledge more generally.
[There are a few ways I could go from here, most of which deviate from the outline in part... Instead of just talking about human cognition in general, as I intended, I went ahead and talked about how prime matter relates to our knowledge. This seemed important for manifesting the difficulty. I could just say "something is intelligible insofar as it is actual", but I wanted to make more clear the meaning of that statement by situating it within the context of human knowledge. At the end, I made it sound like I'm just going to talk about God's knowledge generally... I'll probably do that. I want to talk at some point about how we know singulars, and that account doesn't work for God. That should be coming up soon. Perhaps after the general consideration.]