Suppose I should chime in here as I'm running WPU on two sites.
http://www.tommyvallier.com is my personal blog/site. Most of the customizations are being handled through the WPU admin backend, but I do have an additional CSS file I'm using with a handful of extra tweeks. It's running 1.1.1.
http://www.wpbytheminute.com/ is running WPU 1.1 (Holding off on the upgrade for now). Because it's not running 1.1.1 (and because of some tables I'm using) there are more CSS hacks to make this one work than the other one.
Never happy with the way my site looks, though, I'm tweaking a clean install of WPU for tommyvallier.com already.