Nhancer and the config settings help

[SillyBilly]

When I play quake2 I use "nHancer" to configure my "SLI" and many other settings such as anisotropic filtering, Anti-Aliasing and such. Question is, Do I leave these type settings out of my configs and let nHancer do the work or how does this work. My SLI is working with quake2, I use the "Show Bar Graph" option so I can see it working. Just a little confused, when I go to console and use "cvarlist", I see settings set that nHancer controls and wondered if they conflict.
And whats the cmd for saving the cvarlist to a text file please?