You perform a full wipe of the phone, wipe/factory reset, wipe cache and wipe dalvik cache. If you are coming from a ROM (rooted) you can simply back up the ROM before wiping. Then if things are not to your liking you can restore.
I performed a full wipe yesterday. Used Back Up Assistant before the wipe and used Back Up Assistant to restore all 567 contacts after the installation. Worked perfectly. Then after signing into my google account the Market started replacing my prevously downloaded apps, automatically.
Problem with some ROMs is that old data doesn't mix well with the new ROM. Causing problems galore. I am a newbie pretty much. Thus far four ROMs installed over the past 6 months on various phones. If I can do this you can to! Lots of opportunities out there for some pretty slick themes, etc.