First, unless your playing 3D games, you don't get any benefit from running your memory that fast. And yes 300ish MHz is about ideal but CGMiner probably won't be able to set your cards any slower then core less 100 MHz. So you would need to use something like MSI AfterBurner to set it witch gets to be a pain if you reboot often.

And if you are playing 3D games on that PC, you probably should quit your miner while you play and just re-launch it after your gaming session/marathon.

As for the large performance difference between the 2 miner programs, my guess is that CGMiner is reducing the core clocks on your 6970s. You should be able to check by pressing 'G' while CGMiner is running or better yet, use something that does data logging like GPU-Z to record what happens when you launch CGMiner and compare that with GUIMiner.