In the case you'd share a rig with someone else, how would you set your thing?
Can you start two instances of Claymore's (for instance), one mining with GPUS #0 to #5 to this account and one mining with #6 to #11 with this other account?
Yes, there is absolutely no problems.
2 instances and each with it's own parameters : algo, pool, coin, wallet, GPUs identificaters, worker, password.
You can also use one instance per GPU and have a setting different for each GPU : 3...6...12 : as you want.