I can't speak for roms installed on the sdcard (they're quirky), but if you root your stock rom, or have any rom installed on your Nook, you can back it up with Rom Manager/CWM Recovery.
A roms flashed from this bootable CWM sdcard will be on your Nook (aka EMMC). If you wanted a backup, you'd want to do that first
O/W it's easy to return to stock.
IMO Sdcard installs are fragile (sdcards fail), more difficult to create/update, and slower than roms on the Nook. Most of the guides here are for emmc installs so ask before trying to update your sdcard install if you don't see specific mention of that.