Trem (anything newer then default 1.1.0) uses 2 folders, fs_basepath which is in program files, and fs_homepath which is user specific and by default in appdata. To make trem use a different folder you can use +set fs_homepath "C:\Documents and Settings/username/My Documents/Tremulous"
(on Windows, quotes are needed if there is a space in the path) , and then put any required files in there instead. This folder can be anywhere. If you do change it, make sure you move/copy all files from current home directory there too or you will lose settings & binds.
Either way, you will still have to put files somewhere.