depends on the miner, but just create 2 miners and add the command line option to use x,y,z cards on one miner and 1,2,3 on the other
There may be a more elegant way to do it as well, but the above should work I think
Not sure how to implement your suggestion on AM, really. In NiceHash, I expect to just un-tick the GPUs and they will not be used, but I cannot find how to do the same in AM