Hmm...I guess I would have been in that situation once too.

The MX-900 is a much more powerful remote than something like a Harmony. It was never intended to have a wizard-like setup. But if you give yourself a bit of time to toy around with it, I think you'll get it. The first step for you is to read the manual while trying it in the program. The manual will get more complex than you probably want to go at first, so keep it within reason.

The steps to programming are under the "Program" menu in the software. Use them in order.