Thanks for trying the software. Yes, Hash Auger runs a separate mining process for each GPU for several reasons. First, running each GPU in its own instance allows each mining process to be customized for each GPU - which is great for people that have different types of cards in their rig.  Second, running each GPU with its own miner instance helps isolate errors; if one miner crashes, the software can just restart that one instance while all other GPUs are still mining as though nothing happened.  Finally, depending on the hardware and algorithm, some users have noticed some performance improvements mining with fewer GPUs per mining process because their is less overhead in how the mining program  manages multiple GPU  threads.