Quarto has written a tutorial on editing WCP/SO rooms. If you ever wanted to put Mr Kat in the Midway Rec Room, this article will tell you how to do it.
Each room consists of at least two files - a ROM file inside the \mission folder, which defines all the "hotspots" inside the room, the background graphics, and the animation graphics. The second file is an IFF file containing the background image to be used by the room.
You can read the whole thing here. KillerWave's is a good place to start if you want to modify WCP or Secret Ops. Here's what typical mission code looks like. If you'd like to know more about coding missions and need more guidance, ask Pedro about his WCP Pascal lessons.