hah, i've asked alot of questions about render layers before :p
have you seen the "how do i render a movie?" sticky thread up there?
ragecgi made a really good video on render layers
there's probably something on area autodesk too
to give a straight answer to your question.... yes
never used digital fusion but if its a compositing tool then yes, you can merge yours layers
you can put all you buildings into one layer and put all your trees in another
the only thing you'll encounter with that is you wont get the shadows of buildings on trees and shadows of trees on buildings.
to do that you would put everything on one layer (or everything you would see) and turn off the render visibility in the render stats for all the buildings or trees.
here is the area autodesk tutorial
not sure if it will help, you have to know maya pretty well...
that's a "Ch" pronounced as a "K"
Computer skills I should have:
Maya, XSI, Photoshop, AfterEffects, Motion, Illustrator, Flash, Swift3D