There's two basic routes to go:
1- Just put it in Visualhub (or HandBrake SnapShot 0.9.3?) and use AppleTV preset. Convert for several hours, and be done with it. Personally, in Visualhub I would use AppleTV with setting of high, go nuts will increase file sized with little noticeable effect.
2- Become obsessive compulsive and start learning alot more about the process and details of the various video formats. Wikipedia, Handbrake forum and wiki, etc (read Dynaflash's video posts bc he is one of the developers of Handbrake)
Step 1: Install MediaInfo Mac (free) to learn more about the video you want to convert. It COULD be possible that the actually video and audio streams in your MKV files are actually AppleTV compatible. Which means learning more about the different formats/streams. Sometimes you don't have to convert (streams) but change containers (MKV,MP4,M4V,AVI) This is called remuxing, where you can extract the audio and video out of the MKV container and then recombine them back into a MP4 container. This may only take 1-10 minutes depending on the length(time) of the video.
If you read this far......
1- You're bored, confused and could care less about video formats, then go route 1 and be done with it and don't waste your time, you will still have good results. Run your conversions overnight or when your not using your Mac.
2- If this stuff is interesting to you, Read, Read, Read, and experiment.