One way to configure your Quake client is to change your command line.
This is what parameters you send the program when you run it.
An example of a command line for fuhquake:
C:\quake\fuhquake-gl.exe -width 1024 -height 768 -bpp 16 +cfg_load fuh.cfg
An example of a command line for moreqw:
C:\quake\glmqwcl.exe -width 800 -height 600 -bpp 16 +exec more.cfg
We're sending width, height, bpp, and the cfg_load command to fuhquake-gl when its run.
There are commands that can only be sent in the command line (like width, height, and bpp).
Other in-game commands can _also_ be sent in through the command-line (use a + before these commands).
It's not a bad idea to set your config file to be loaded on game start.
If you use morequakeworld, instead of +cfg_load , use +exec .