By onboard and external, you mean integrated and dedicated? CGMiner should mine on any GPUs you have, unless you specify otherwise.
Thats what I mean yes. But how would I set my .bat file to do them both tho as I only know how to set up for one.
cgminer -o pool -u username -p xxx --shaders 1600 --intensity 14 --worksize 256 -g 1 --auto-gpu --gpu-memclock 310
If you use one variable, it adds that variable to all your cards. If you want to specify different values for different cards, you add commas between your values.
Try this:
cgminer -o pool -u username -p xxx -I 7,9 -w 256 --auto-gpu --gpu-memclock 310,305
--shaders only works when you're mining litecoin, but if you're doing that, then you don't want your mem that low. I: higher than 9 can sometime cause high CPU usage, and you won't get any faster results, again, unless you're mining litecoin. And lastly, -g 1 is only really useful if you're using p2pool, or dynamic intensity.