There are different ways depending on what kind of system you are looking at, but fundamentally it's quite similar to the bulk case, except you have more "materials" involved. If your central region e.g. has a molecule and you are transporting through that, you want to compare the transmission peaks to the molecular eigenvalues (HOMO, LUMO, etc). If it's a bulk structure ABC you need to compare the DOS and projected DOS between all 3 materials.
I would suggest looking at published articles involving similar systems as yours, and checking what analysis they do. If you have trouble carrying that out in the code you can ask more specific questions.
