You can just have a separate config for each card type and specify the devices you want to use with it. Check the --device option in cgminer. I run 7950 and 280x in the same rig with no problems.
Or make two workers at your pool and create two batch files like the following (assuming your cards are named 0 and 1):
cgminer --scrypt -o stratum+tcp://yourpool.com:port -u you.worker1 -p x -d 0 --remove-disabled
cgminer --scrypt -o stratum+tcp://yourpool.com:port -u you.worker2 -p x -d 1 --remove-disabled
Of course you can tweak and add your settings but this should get them running. You'll have 2 instances of cgminer with settings customized for each card.