Even if you have iTunes set to manage your media you can override this by holding down the option key while dragging items to iTunes. It will leave them whever you put them.
Letting iTunes manage your media you cannot have two media folders designated at one time. You could designate one, consolidate items to the one, change media folder location and selectively consolidate some items to the other and split media this way.
If you do not let iTunes organize your media for you then it can be pretty much anywhere. I do not let iTunes manage my media and I used to have it on 2 separate drives. Right now I have it in 3 major folders outside the iTunes folder.
Absolutely do not just move the music in Finder. You'll break iTunes that way. If you want all your tracks in a single place, make sure the correct location is selected in the Advanced preference and then use the Consolidate command. That's what it's for.