I am not entirely sure if I understood your question correctly, but here it goes:
I thought it is possible to run multiple miner instances for multiple algos on a specific subset of cards just by using the right commands without sniffing software. In ccminer you do it with -d DEVICEID, where DEVICEID is the number of your CUDA devices you want to actively run. Did you try that? Or is that already causing the problems? I would not use that split software if you don't have to.
I also suggest (depending on the algos you want to use) to try just the pure EWBF's miner and Palgin's ccminer mod (not the alexis mod). They are both more optimized for CUDA cards, especially 1080's. The newest release was just recently upgraded to CUDA 8 which should give you a slight performance increase.
Always switching around in the pools is not something I favor. I rather mine a coin for a week and switch afterwards. At least with the pure split command you could mine 2 coins simultaneously with 1 rig, which is already sweet.
Hope that helps