You will need to create a custom profile to do this. MCEBuddy can differentiate between AC3 and non AC3 input streams. See this topic for details:
Basically depending on whether you’re using Handbrake or FFMPEG you would need something like this, this keeps non AC-3 audio stream as is and converts AC3 audio into AAC
handbrake-audioac3=-E faac -R auto -B 384 -a 1,2,3,4,5
handbrake-audio=-E copy -a 1,2,3,4,5