you start 2 instances of cgminer. each with its own settings. check this forum i posted a few questions regarding this. i still have to figure out some things.
cgminer.exe --scrypt -u user.6850 -p pass -o [Suspicious link removed]:8888 -u user.6850 -p pass -o coinotron.com:3334 --thread-concurrency 6144 -w 256 -v 1 -I 16 -g 1 --temp-target 75 --lookup-gap 2 --auto-fan [b]-d 0[/b]
cgminer.exe --scrypt -u user.7970 -p pass -o [Suspicious link removed]:8888 -u user.7970 -p pass -o coinotron.com:3334 --thread-concurrency 6144 -w 256 -v 1 -I 16 -g 1 --temp-target 75 --lookup-gap 2 --auto-fan [b]-d 1[/b]
you cannot do all this in one conf file unless both your GPUs require the same number of GPU-THREADS. if your gpus require 2 different numbers of threads then you cant do it in CONF file because the GPu-THREADS parameter only takes 1 argument. can't pass two