I'm pretty new myself, but I do basically that except I only put the doorway pages into new folders, the main and gallery pages I leave in the root folder and I have never gotten rejected for directory structure, I get listed pretty much everywhere everytime I submit - I think I just got the fastest acceptance email ever;p I submitted a site to Link O' Rama and got an acceptance email not 5 minutes later
Must have got it in at just the right time. Anyways if it makes it more clear my setup is like this:
boobs/main
boobs/gallery1
boobs/gallery2
boobs/tits/index
boobs/melons/index
boobs/knockers/index
if that helps at all.