I am on the verge of snagging a nook color (once it is released) but I still have questions as well and this is one of them. I'm afraid my in store employees lack knowlege on details us "hard core" nook lovers need to know about the nook Color.
@WilliamHartnett: There is a "My Files" option in Library that will show you the folder layout for sideloaded documents. However, if you place your ebooks under the folder "My Files/Books", they'll also show up in the "Books" section of the Library, combined with your B&N purchases. It doesn't matter what subdirectory they are in, as long as they are under "My Files/Books". This works for the on-device memory as well as for the microSD card.