Aha, that's the missing link - the config command. Thanks Bandures.

Okay, so if anyone else wants to know, here's how to make a map that runs on it's own:

1) make your map  

2) create a config file in your mod folder and call it anything you feel like (although ending in .cfg is recommended for clarity). In this config file you need one simple line:

map mapID unitID1 unitID2....unitID5

where mapID is the ID number of your map, unitID1 is your hero unit ID, and unit2 through unit5 are your team units IDs.

Save that as plain text format.

3) Create a shortcut to silent storm's game.exe file. How you choose to get this shortcut to other people is another matter. The shortcut needs the following paramters:

game.exe -gamedir modName -cfg ./modFolder/configFile.cfg

modName is the name of the folder in which your mod is created. modFolder is also the name of your folder mod. the ./ is needed as the ./ tells the game to start looking in the root silent storm folder instead of the cfg folder. Also, ensure you include the extension (.cfg) in your parameters, it won't add it itself.

Double click that shortcut and you should be taken straight to your map and have the units you selected. Map based scripting is required if you want the units to have more than basic skills and equipment though.

As I mentioned, getting the shortcut to your players is another matter. I'm currently looking into making a mod organiser that will allow users to select maps and mods to play before starting silent storm with the appropriate parameters. More news on that when I get around to making it