OK, I have this set up now. BFGMiner is running the USB ASIC for Peercoin and cgminer is running the GPU for Litecoin. I also have cudaminer running my second GPU for Litecoin, which was necessary as cgminer didn't like running two different GPUs at once. All works nicely together now.

Assuming your computer has enough CPU, memory and network bandwidth and separate computer processes will be used for each form of mining, it should be nothing more than associating the right hardware devices with the right miner software. Be careful to not transpose things...