I finally figured out how to do this today.
Here is how I did it and it appears to be working:
Go into the Nvidia control panel (right click on the desktop)
Go to Manage 3D settings
Select Program settings
Click “Add”
browse to c:\program files (x86)\plex\plex media server (or wherever you have it installed).
Choose “Add Current Folder”
When you are back to the list of settings you can adjust, change “CUDA - GPUs” to select the GPU you wish to assign to plex.
I also turned “optimize for compute performance” to On. Not sure if that makes any difference, but i figured why not. 
I restarted plex and verified through Task manage that my GPU 1 was being used when I did a stream that uses HW encoding.
