On regular MultiPlayer files, you can use "SH4MissionEditor.exe", which is found in the same folder as the game itself, "SH4.exe", and open one of the files in the "MultiMissions" folder. The "ADVXX..." files are the adversarial, while the "MPXX..." are co-operative. You can move the boat icons and ship icons around, but you'll find that most of those files have "set" groups. For variety, you'd need to use Random Groups. As for the "Custom Map", I haven't seen a way to alter that. It looks like, to me (and I'm no expert), that it is hard-coded. Someone else probably knows more...
