Everything you need to run MMM and single player missions is in the MMM mod folder download. You can use this just to put missions in, or you can use it as a guide for your own mods. The mod folder is available here.
Copy the mod folder into your FleetOps/Data/Mods folder to install it. You can then activate the mod by going to the mods menu in FleetOps.
An understanding of Lua is required to use MMM. You can learn more about Lua at http://www.lua.org.
You can read more about the structure of MMM here. Also you should take a look at the API Reference for a complete guide to all classes available for you to use in your scripts. For tutorials on various topics, check out the Tutorials page.
For writing your scripts, a syntax higlighting editor such as Notepad++ is recommended.