Noesis appears to have difficulty reading information for models that do not exist as a single, self-contained file. This means character models for NPCs work just fine, but models for player characters don't work. Or at least, I haven't figured out how to get them to work. Maybe I'm just not using the program correctly. I dunno. I'll have to experiment with this a little more.
Nope, you can read from multiple streams if mesh information is stored across multiple files. See NoeBitStream.
Edit: Take a look at my Rise of the Tomb Raider mesh importer. I load skeletons from a different file. Should be enough to help you figure out how to create multiple file streams.