Maybe I'm a total idiot, but I can't figure out how to alter the settings on a map made for fighting against the other player in hotseat and convert it to a map in which we are allied against the computer. I can change the settings so my son and I start the game as other colors, but it will not let me alter it so we fight on the same side (unless the map was designed for hotseat allies; most are not).

I think it's possible, because other posters on this board have said so, but how do I do it? [crosses fingers for simple explanation]

I'm willing to create some allied map versions if you can tell me which game you have (original or which expansion) and also if you would be able to unpack the zip file and put all the maps into the maps folder?

Have you tried changing Team setting in editor?

View-->map properties--> Teams

If 6 players on map make 5 team. Put you and son on one team and each other player on team by itself.