Install over exisiting vista question

I have clean installed vista retail upgrade on a couple of PC's in the house
by doing the published deal of booting with the CD, installing without the
product ID and then installing again via windows as the upgrade with the
product ID. All so far, AOK. On my 4th one, I accidentally skipped the
step of doing the upgrade from the clean install and went on installing
users, office, other files, etc. Now I realize I didn't activate it, it's
prompting and I cannot because my product key is only good on upgrades. My
question is, if I upgrade from this current install, will it overwrite my
two user accounts, email, office install, etc? Thanks.