You shouldn't have to, if you know your way around hte .upl yu'll see it's got a body texture and it states there where to find the body texture, this is how it knows what texture you skin uses, this much i expect you know, it onlyl needs to know this much, ut itself assumes that your teamskins names are (the name of the body skin)+_0.
The textures you imported should be the same name as your normal skin with the "_0" or "_1" extension. Example!
If your skin name is! (Defaultskin!)
Defaultskin_0 (For red)
Defaultskin_1 (for blue)
It's a lot simpler than i explain it but if it still doesn't make sense look at the way the .upl for the default UT skins are and how their .UTX folder is made that might help.