Yes you should be able to assign a specific GPU to be used by SD, though I'm not sure how it works with both an Nvidia and a AMD.
Anyway, one of the two gpu will be used by the substance engine (for the compositing work in the graph), it can be the AMD or Nvidia it does not matter, we don't use CUDA.
For Iray, if you have an Nvidia, it'll be used, even if your monitor is not plugged to it.