Yes, you can make a NAND backup at any time. It will save the exact state of your system and then you can restore it later.
I do it all the time when I'm switching between ROMs, because I too have them all customized exactly how I like. In fact it's usually the only method I use to backup because its so fast and convenient.
I have a 6 gig microdrive and it doesn't work for backup or restore. I have a theory it's beause the format is FAT32. I usually use 1 or 2 gig cards for this purpose.