Ah, that's easy. Just put eight player starts on the map and have the players select the correct faction at the beginning.
First player in the lobby always gets all of side 0's units and structures, second player gets side 1's, etc. So if you wanted to 2-player co-op for the Atreides campaign, just make sure the AIs are using sides above 0 and 1. You can also force the player start to not spawn MCVs or any units with ini settings so the players only begin with what's on the co-op map.