I know with BFGMiner, you can specify which gridseed to use by selecting the COM port it's associated with.  I think for CGminer (it's been a while since I've used it) you can select just 1 gridseed, using something like --gridseed=\\.\COMx to select that specific gridseed.  Then open the second instance and use the other com port that the other gridseed is attached to.  I can't remember exactly how to run it because I use BFGMiner and Luke-JR answers those questions super fast.