For one, I continue to hear many atheists say that quantum physics somehow disproves Aristotelian metaphysics but I never quite hear an explanation how or even a good understanding of Aristotelian metaphysics for that matter.
That is not necessary. As Carroll rightly states, your metaphysics must follow your physics, and Craig's metaphysics is stuck to 2500 year old physics.
Don't be misled by the etymology. Andronicus called the work "metaphysica" in his edition of Aristotle because it was the book that came next in the corpus "after" the Physics. The Latins misunderstood this to be Aristotle's title and took it to refer to those things that are "beyond" (i.e., foundational to) physics. Though the Latins misunderstood the meaning of the title, they clearly understood the theme of the book: it is the book about those things that are foundational to physics and all human thought and rationality. This is why Aristotle referred to it as "first principles." In any event, the discipline represented by the English word "metaphysics" does not deal with "that which follows physics." Carroll is simply confused. On the contrary it is metaphysics that is foundational to physics.
For example, does Carroll think that physics is foundational to or must precede numbers and mathematics? Surely not. Without numbers and mathematics there could be no such discipline that we call physics. But numbers and math are part of metaphysics.
Does Carroll think that physics must precede the basic rules of inference or replacement? Surely not. Without modus ponens or commutativity the discipline of physics could not exist. But basic logic is part of metaphysics.
Does Carroll think that physics must precede the rules of induction? Surely not. It is hardly possible to imagine a more important tool in the physicists tool box than induction, but the theory of induction is part of metaphysics.
Does Carroll think that physics must precede the principle of numerical identity of objects (not to even mention persons) through time/space. Surely not. There could be no physics without it, yet it is clearly not a deliverance of physics itself. It is a metaphysical concept.
Does Carroll think that physics must precede the concept of physical laws or laws of nature? Surely not. There could be no physics without it, yet the concept is clearly not something discovered by physics. It is a metaphysical concept.
Does Carroll think that minds other than his own exist such that they can read his physics papers, or write the papers that he reads, or talk about physics problems with him? That assumption is essential to the discipline of physics, but it clearly is not a deliverance of physics. It is a metaphysical concept.
We could go on and on with questions about time, history, memory, perception etc. In some way or another physics depends on these concepts, but none of them is a deliverance of physics. They are all metaphysical issues.
The same can be said about causality. It sounds sophisticated to say that physics does not use or need the concept causality, but this is simply a confusion. Whether physicists use the word or not, what Aristotle meant by "efficient cause" is employed constantly by physicists. The discipline could not exist without it. The denial of this only sounds plausible because it trades on the ambiguity that exists between material and efficient causes. Aristotle's language may be out of style, but the distinctions in question are simply fundamental to rational discourse of any kind, including that discipline we call physics.
One last thing. It simply is not true that philosophy is not discovering anything while physics goes marching forward. The dilemma is posed as if philosophy is somehow impugned when it makes no advances in astrophysics. But that would be like saying that physics is irrelevant because it hasn't told us anything about the fall of Rome. Philosophers are not supposed to be doing the physicists job for them. They might tell them when they are straying beyond the bounds of their discipline, or help them better conceive the scientific method, or debate with them about the metaphysical implications of their findings. But philosophers are not supposed to be actually doing the physicists job for them. Philosophers do philosophy. And they have in fact actually done some pretty remarkable work over the last few centuries. Look at the advances in logic and math (Frege, Russell, etc), philosophy of language (Wittgenstein, Austin, etc), philosophy of society (Searle), more debatable perhaps but still worth mentioning would be epistemology, economics, and even psychology/sociology/cultural anthropology. Some of these like to put mathematical equations in their texts to make themselves look more like physics or chemistry, but they clearly arose from, and in the end they are best considered as branches of philosophy. Like every discipline, physics has a high opinion of itself, and for good reason, but physicists shouldn't think that there really are very many people in the world outside of a few small intellectual circles who ever spend any time seriously thinking about these things. Physics and philosophy are both highly technical and often quite obscure. Most of the world couldn't care less about the things that most excite both philosophers and physicists. The relevance of their respective research projects is not immediately obvious to outsiders, but to those who have acquainted themselves sufficiently with the issues, we believe that they are quite important. A moment's objective reflection by a physicist on his own discipline however, should give him pause before he begins mocking philosophers for their "obscure," "abstract" "mumbo jumbo. Those who live in glass houses shouldn't throw stones.