In the past whenever I did separate CPU and GPU mining I had to configure it to use all the cores except one. Basically if you try and mine with all cores on the CPU, your GPU speeds will slowdown.
So if you got a 4 core CPU, you need to configure it to mine with 3 cores and leave the last one unused, the last one will be used for the GPU mining. Most GPU miners don't need a lot of CPU resources however if all CPU cores are using 99% usage then the GPU miner will lag from time to time and you will get a slower speed.
Sorry this is wrong. We mining with all cores on our rigs (Intel G3900) and the gpu´s didn´t slow down.