The biggest difference between multiplayer maps and skirmish maps is that you have to add an AI (Artificial Intelligence) player that will control the computer opponents, and you also have to mark some areas on the maps to make the AI able to make qualified moves.
Basically you have to mark off an Inner perimeter around each players starting point, where the base will be built. Around this you mark off an outer perimeter where the AI will build defences. There is a video here that will show you how to convert the map made in Making simple multiplayer maps into a skirmish map.