Is there a way to set a different username/password for each GPU so I know what's working and what's not from my pool workers page?
Nice edit.

Glad you figured out your original issue. Regarding this one, you could run separate instances with a specific GPU selected for each instance. If you want it all in one instance, you brought up a good reason why it would be useful to choose resources per worker in the command line. Unfortunately, I don't think it's currently possible (refer to my response to another question in this thread just a few posts up).