If you haven't read "Program MARK A Gentle Introduction", then you should do this before going further. Evan Cooch at Cornell University is developing this electronic book. For the complete novice, this is the place to start to learn how to run MARK. This guide is a work in progress, so is not complete just yet.
Be sure to read and work the examples in the Gentle Introduction before trying to analyze your own data.
You may be able to get help from the MARK listserv as well. Read the FAQ before submitting your own question.