I tried and it semi works, err well it leaves the -cqp setting in the main cmd line. I'm guessing the 2 fight with each other. The results have been odd.
After 7 test conversions adjusting both, they both seem to still be functioning.
Normally I would use straight x264 but the last few build's of mediacoder seem much slower when using x264.exe. Both ffmpeg via mediacoder with exact settings and megui using x264 are on avg 16fps faster "20+ in some cases" when converting the exact same media/res/adv settings. Megui is a killer app but it requires to much input per encode. eg open file / check the res / change the res / autocrop / save / auto encode / choose yet more crap / send to queue. Then do it all again GRRR... And that's after setting up all your presets. srsly wth is the point of presets if you still have to do all that... I get great results with it but I'm pretty sure it gave me carpal tunnel...