> How do you upload .bres files into MilkShape3D?
You can't (although I may write a tool to convert that direction)
The current MilkShape3D technology is primitive. You create a 3D model from scratch, then I have some tricky tools to convert it to AC:CF game compatible item models (which can then be retextured if necessary).
Right now the models I'm testing are simple spheres (spinning poke balls), but the approach can work on other 3D models as long as they aren't too big.