You need to encode them using Handbrake or some other video converter. If you do a search for Handbrake you will find all kinds of threads, both here and on Google.
After you convert to a compatible format, I think you can just have your iPad connected to iTunes and then left-click and slide the file to your iPad in the iTunes software. You may have to create a movie folder and then add that folder to iTunes (more involved). Good luck.