Thanks again for the feedback. Here’s the workflow for the skull -

1. Sculpted the basic shape from the existing head. Since the bone dictates the shape of the face to such a large degree, it seems to make sense this way, since a lot of the skull is already modelled.
2. To topologise this into 2 parts, I needed to seperate the mandible from the main skull. I masked the jaw, and cloned the model. One each version of the model, I smoothed, moved, and flattened away the part I didnt want to retopologise.
2.5 This step isn’t in the picture, but now having 2 seperate models, i hid away the rest of the mesh, and then closed up the hole where it attached.
3. Topologised those 2 parts seperately. I did it in all in zbrush, but certain things would be easier in maya or an external package. For example, if I’d wanted the zygomatic arch (cheekbone going back to the ear) to be seperate from the rest of the skull, like it is in reality (ie you can stick your finger through the hole it creates), there’s no way I could do that from that mesh in zbrush.
4. Sculptsculptsculptsculptsculptsculptsculptsculpt
There are pretty big issues with this method, though. At least there are if the topology is of any real importance. For example, the inside of the jaw was reaaally messy, making it difficult to retopologise. Again, if I’d been particularly bothered by that, I’d probably take it out and finish the topology in maya, or maybe do a basic topology, sculpt it into shape, then refine the topology in zbrush.
Another side effect of the jaw being so messy was that projection didn’t work (which worked well on the main skull). That wasn’t a problem, since the details were so rough to begin with. If I’d wanted to keep the details, I would’ve done the topology as normal (maya or zbrush) and later used the “project all” button in the subtool menu to get my details back. I love that button, and I think in it’s own cold, quiet little way, it loves me too.