I just copy it to Scenario folder. Filese with MS and MU extensions are found in Missions menu in the game. MC files are part of campaign. Each campaign needs one more file with CAM extensions. Campaigns and their missions are visible in Campaign menu.
What may confused you is that some campaigns (RSR too AFAIK) contains both MC and MS versions of the missions. You can either play whole campaign, or individual missions alone.
Difference between campaign and single (or user) mission is that campaign missions must be played in defined order and platforms killed in one mission will not appear in next missions.
Difference between MS and MU is that only MU missions are editable in mission editor. Just rename for example "Kilo demo.ms" to "Kilo demo.mu" and you'll be able to open it in mission editor. There is no other difference.
There is also MP extension for multiplayer maps. Again, no difference against single missions, but these are offered for multiplayer matches. You can play Kilo demo in multiplayer if you modify the extension and mark FFG as playable in mission editor.
I guess there is some extension for user campaign missions, I don't remember.
Also note that missions can use custom WAV files. Such WAVs are included in mission archive and they too should be placed in Scenario folder.
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