I have a couple of movies I would like to convert from MKV format to ipad friendly MP4v.
The mkv movie is in HD and is 6.5gb in size.
Using handbrake significantly decreases the file size and quality.
Any ideas how to maintain the quality after conversion?
Usually increasing the video bitrate setting will increase the quality, but it will also increase the file-size as well.
There are a few different video formats that Handbrake can use. Make sure you use H264/x264. the FFMPEG format is a bit faster to convert, but doesn't offer the same compression (quality).
Another option is to reduce the screen-size a bit. This might sound strange, but if you want a smaller file-size while reducing quality issues to a minimum, going from 1080p resolution (1920x1080) to 720p (1280x720) will enable you to reduce the size considerably, and while the video doesn't look as sharp as it would at the full 1080p, you can probably go down to 2GB for your movie while still having it look great.
A week or so ago, I wrote an article on this that gives some better insight on that:
http://www.ipadforums.net/dvd-catalyst/79858-tip-how-make-your-video-files-smaller.html
Another option is to use CRF.
This automatically adjusts the bitrate to whatever is needed for the conversion to keep a certain quality. This article can shine some light on how that works:
What is CRF? | Tools4Movies | DVD Catalyst 4