Well, You have the standard Inbox... in the "root"-directory together with the Outbox & Sent yadayada..
I don't think You can have additional custom folder in that root-directory but You can always use new folders "under"/inside the Inbox.
Say like "Inbox -> Domain1-Inbox, Domain2-Inbox, POP-account@ISP, bla-bla..."
This is what I have and it works excellent
