Sorry didn't notice your post until now.
Vista will quite happily install the game wherever you specify in the game setup. I don't know why the game would have reinstalled back into Program Files, unless you didnt change the default.... it won't automatically find a folder on your hard drive named Ubisoft. And you don't have to create the folder before you install, it creates the folder you specify in the custom setup. Unforunately I'm not at my gaming system right now so I can't give you a step-by-step, sorry!
In short, before the game started copying files, you should have seen where the game will install by default into the Program Files folder... at this point you click Change (or is it Browse, I can't remember) and then you either type a new location (such as C:\Ubisoft) or if you previously created the folder you browse to that folder and it will fill it in for you. Probably best to just type it then you can be sure.
Hopefully you get it figured out, or someone that can explain things better than me comes along to help you
Note: make sure you uninstall the game from Add/Remove Programs (or the games Uninstall utility) before you try to reinstall again.