I can't seem to figure out how to tell BOINC to use the CPU, but not the GPU while my PC is in use. Reason being that while things are able to take back some CPU from BOINC while it runs, the GPU does not seem as forgiving, and leads to either turning off GPU altogether, or turning off both CPU and GPU while idle, both unfavorable options.
Any help?

In Computing preferences:
- Suspend GPU work while computer is in use? Yes.

In Local Preferences:

Uncheck Use GPU while computer is in use.

These preferences require that BOINC runs CPU and GPU based on preferences.
They also require that boinctray.exe is running. This is the idle tracking program.

If this doesn't stop the science application, complain at the forums of the project that the science application is from. Then their application isn't adhering to the suspend request that the client sends, and it's out of our hands.
When it's a Seti or Einstein application, check their forums first for threads about this subject.

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Oh, right. Sorry, I missed it. One more question: Does joypad input count against the PC being considered idle, or would I need to press a key on the keyboard once every hour or so?