Handbrake uses Intel QuickSync and FFMpeg uses NVidia acceleration.
If you’re using a profile that uses both ffmpeg and handbrake, MCEBuddy will check which hardware encoding capabilities exist and will automatically use the hardware accelerated encoder first. So if your profile has both ffmpeg and handbrake, it will test to see if NVidia acceleration is supported and then it will use ffmpeg first.
Most profiles have both ffmpeg and handbrake so it should pick it automatically if acceleration is working.
The log files will give you more information about what’s going on.
More details here: