Hey Koldov, let me try and get you some answers (better late than never).
I would strongly recommend using GP Preferences when possible over GP Polices. Why? Preferences has bigger hooks into the operating system than Policies does. It can do more and do it better, more consistently and faster than policies. It is essentially the modern take on GP Policies (they date back to the NT days).
User configuration and Computer configuration are simply different categories of Group Policy. Both will be applied no matter what inhabits the container Active Directory where you are apply your policy. The difference being User configuration is applied to those specific users regardless of the computer they log in to and Computer configuration is applied to those specific computers regardless of what user logs in. The other difference is computer configuration is applied before the netlogon (CTRL+ALT+DEL) fires up where as User configuration is applied upon the login of a user.
Hope that clears up a few things.
Thanks for linking to my blog btw. Glad to see it has helped some people out!
EDIT:
Ah KiX scripts. The very first thing I killed when I was given the reigns and discovered Group Policy...
