If you are talking about autogen.cfg you're right: this file is automatically generated by tremulous, but on my system (linux) seems to keep track of previous settings.
I'm a newbie like you, but I found the
config fest post and this made me think.
It seems that if you put a file identical to autogen.cfg but named autoexec.cfg, this file will be executed when you start tremuolous.
I split my cfg file in many pieces, using "exec", like this:
autoxec.cfg
exec generic.cfg
exec autogen.cfg
exec mouse.cfg
exec keypad.cfg
exec talk.cfg
and then I created generic.cfg (with generic bindings), mouse.cfg (with mouse bindings), keypad.cfg (with keypad and extended keypad bindings) and talk.cfg (with quick talk bindings)
... and it works
Maybe this is not the answer you were looking for, but try to modify autogen.cfg and rename it autoexec.cfg (autogen will be restored automatically) and see what happens