http://tbruckner.esmartweb.com/misb4/index.html
There's alot of support for this program in the forums here.
I'd recomend learning the program by building some simple sim missions, gradually making them more complicated. This will teach you /most/ of what you need to know about mission editing and allow you to have some fun while you're at it.
This program works with Secret Ops or with Prophecy, but my understanding is that most people learn it with Secret Ops because everyone has secret ops (or can get secret ops) which makes it ideal for mods for the community.
If you're going to use secret ops though you need to install a patch to include the simulator in the game (this patch can be downloaded from the CIC's download section, where you can also get the secret ops main package).
Lastly, I recomend exracting all the .tre files for the game too, as this will aid you a bit in your development (especially if you want to add more ships or edit the existing ones to make them fit your mission). This step also makes it easier later on to build a campaign using the files you create.
The TRE files are compressed files that store all the data for the game, missions cutscenes voices ship data, so on and so forth. The nice feature about Prophecy and Secret Ops is that they look in the directories in the game directory first, then check the TRE files if they can't find a missing file. This allows you to edit the game without really taking it all apart.