Well, I did the EXACT same thing on my Fujitsu computer and was just as clueless as you are. In fact, I believe you're a little more computer saavy than I am as I didn't know anything about partitions. Anyway, I went from XP SP1 to Vista Ultimate 32-bit. All in all it was a pretty good transition however most of my Fujitsu drivers and services stopped working...such as the application panel located above the keyboard, the Fujitsu driver updates, and the integrated wireless adapater (Atheros AR5600X).
This didn't bother me. I never used the application panel anyway. And since it doesn't work now, I guess it doesn't need updating either.
I actually tried for about a month to fix the wireless adapter and then decided it was just best to disable it in device manager and install a more modern and faster USB wireless adapter. The old Atheros AR5006X could do 802.11a/b/g while the new USB wireless adapter can do 802.11g and 802.11g(mimo). Eventually, I'll get one that can do 802.11n...and so on and so forth.
Actually, I'm using the Fujitsu computer right now to reply to your post. I really like Vista Ultimate. By the way, I don't have a super computer or anything like that...it is a Fujitsu A3040 with 1.5 GB RAM, a few USB ports, CD/DVD slot, PCMCIA, SD/xD/PRO/M slot, etc. (pretty standard stuff). It works fine and it does what I want it to do, so I am happy.
A piece of advice...back up ALL of your files somewhere safe just in case your computer crashes during the transition. Trust me on this one, it will save you a lot of headaches and time.
Good luck.