I've been struggling with this for days as well. As far as I can tell Military and Civilian objectives only support one faction, you have to make an mil and civ objective for each faction and sync with the AI commander, which has all the factions you want in the faction list for that side (comma delimited) and then of the OPFOR AI commander

Now I am struggling with the faction setup of RHS, some factions are missing types of units so if you put them in, you'll get a message stating it can't find a unit type (mechanized, armor, sea, etc). Alive only supports the msv and vdv factions, so some RHS units can't be used in Alive modules.

1. RHS organizes its units into many factions
2. Alive uses factions to determine deployment, when trying to use a faction without certain types of equipment that Alive wants to deploy, you will get a message saying as much. At that point Alive may deploy non RHS equipment to fill the gaps, IE IFRIT, HEMTT, etc.