You could also run each instance as a seperate user, since the default location for configs is $HOME/.tremulous/
As far as qvm's, trem has the equivalent of a $PATH variable that may in fact be named path

Trem searches through the path for pk3s, qvms and I don't know what else. The $HOME config directory is the last area searched, so try putting server specific things there (configs, qvms or even maps). You can even copy the whole tremulous game directory (or just download the zip) and run it from within the user home directory. That way its search path would be
$HOME/.tremulous/base
$HOME/.tremulous/
$HOME/tremulousbinarylocation/
So it would load things in the home config, but still find needed pk3s in the "install" directory.
etc, etc. You get the picture. It will gobble up more space and make managing it a bit of a headache, but it will work in a pinch to get the damn thing running
