There is no rule to filter on the encoding type of the media file or file size. It sounds like all of his files are MKV, and the filenames don’t tell you which are MP4 and which are H.265/HEVC.
So he will have to have two different locations setup - one to hold the files that are under 500MB and the files that are over 500MB, and then have the MP4 task only process the folder with the under 500MB files in it, and the HEVC task only process the folder with the over 500MB files.
Probably best to do this via the CLI so that your script can “remember” where the file came from so that it can put the output file back after it has been processed instead of trying to force MCEbuddy to figure that out, especially if your files are already in some sort of folder structure (e.g. for Plex or Emby).