This particular preview copy is limited to fiction manuscripts, but the full software supports fiction, non-fiction, scriptwriting, poetry & lyrics, and "miscellaneous." It won't allow you to necessarily side-by-side notes, references and draft copy, BUT, it DOES have a little side window for references (a la links) and does have a short window on the side for brief notes. So... kinda?
It's customizable to an extent, so I encourage you to check out the regular version (NOT the NaNo preview) and poke around in it to see if you can get it to do what you want.
And it can save (actually, Export) to a .doc Word format just fine (as well as RTF, TXT and Final Draft).