A cool thing here is that MCEBuddy will automatically analyze the graphics cards/drivers capabilities and tries to match the hardware acceleration (for encoding and decoding separately) to the systems’ capabilities and the codecs involved in the profile (custom or stock, including handling multiple graphics cards).
If you aren’t happy with the plug n play option, you still have the option to create highly customized profiles that are tuned for your systems hardware acceleration, which MCEBuddy won’t try to further optimize. Check the advanced commands topic for more details, specifically the UsingHardwareEncoding option on how to create such customized profiles.