If you open your conversion logs it’ll show the exact command line passed to ffmpeg. If you’re using a special build/version of ffmpeg you can always replace the version that ships with MCEBuddy in the installation directory.
If you’re creating a highly customized version of ffmpeg video and audio parameters and don’t want MCEBuddy to adjust any of them (MCEBuddy adjusts them based on your configuration you’ve set in the Converstion Task page like Quality sliders, Optimize video, Audio track selection etc), you can tell MCEBuddy to keep your profile parameters as is with these two ffmpeg directives (similarly for other encoders also):
You can pretty much do anything with MCEBuddy and I would highly recommend taking a look at this page for tweaking your settings: MCEBuddy - Advanced Settings, Commands and Tweaking