Dude you can choose however you want to run your speakers ohm wise as long as you dont go lower than what your amp can push and as long as you run them at the same ohms per amp. meaning if your gonna run one speaker at 2 ohms for amp1 then the other speaker has to be ran at 2 ohms also and the same goes for if your gonna run a speaker at 4 ohms. just make sure the other speaker is ran at 4 ohms for the same amp.
If they are two dif subs they will sound dif anyways it just depends if they can handle the higher rms wattage.