I turned on the onboard GPU in the BIOS, and then installed the latest video drivers for my CPU's GPU. Then after booting I let the system create a faux monitor for a third monitor, with that monitor being connected to the Intel GPU. The faux monitor shows up as non-PnP monitor. It doesn't work with the faux monitor disabled.
After that I made certain that Quick Sync was enabled in the software I was running and that I used the Quick Sync encoder codec. My transcoding frame-rate went from 20 FPS with 100% CPU to 250+ FPS with 60% CPU. The time went from 2.5 hours to 15 minutes!