Unless you're doing an update to a ROM you already have (and moving from a stock ROM to a deodexed version of same ROM doesn't count), you have to wipe both -- up to 3 times. When I say update, I mean moving from Simply Stunning 4.8 to 4.9 or Ultimate Droid 2.3 - 2.4, or flashing CyanogenMod 6.1 stable to a nightly. So yes, you'll have to wipe. Possibly 3x factory reset.
Jon; either use the method in my signature (and yes, I'm aware you're already rooted, but we work with the tools we have), or flash Clockwork/SPRecovery from ROM Manager, do a battery pull, and then reboot into recovery and install the update.zip from Moto's rooting method.