I would highly recommend that you NOT restore any programs or system settings from ROM to ROM, even if the B/U program says it can. Even if things seem to go well at first, my experience is that something will go wrong eventually. You'll probably have to do a hard reset to fix things in the end, so bite the bullet and install everything fresh. Consider it an opportunity to update your old wares and experiment with new options/settings. If you want to auto load your programs, check out
sashimi or the many UC tutorials around here and xda. If you need to restore from a hard reset or replace your device (and first flash to the same rom), then whip out that b/u and have at it.