A:
I recommend a free program called Calibre for managing your non-BN-purchased e-book collection. It recognizes many different e-book readers, handles many different formats, and even lets you convert between formats (so, if you have a PDF, but don't want to use the horrid PDF reader in the Simple Touch, simply convert it to epub format and load that).
When you have your Nook connected (with USB), it will even show you which books are currently on the device. It has support for managing books stored either in the internal memory or on the SD card if you have one installed.
About the only thing it doesn't do is handle DRM-protected books, but for anything you purchased through BN, that's managed automatically by the Nook, so that's no problem. For handling DRM-protected books (e.g. books you check out from a library) you'll probably need to use Adobe Digital Editions to authenticate and transfer it to the Nook.