Then maybe it's time to learn :P
x264 is definitely better. You may have been using an old version of x264 with Mediacoder, and Handbrake's last binary is from February.
For batch processing with x264 (and many other kinds of processing) you can use MeGUI.
You can learn about x264's options at
http://ffmpeg.x264.googlepages.com/mapping, though it may be a bit overwhelming if you've never really used x264.
Just ask if you need help with that, we'll all be glad to help you.