I think what Tree Puncher means is that he wants to set up two factions where he could join and his friend could join the other. He wants to create an npc army that will attack his friend's army, but his friend's army won't attack him.
He basically wants to know how his friend could join one npc faction and he could join another and they could both fight amongst their npc armies without one of the armies attacking the player.
Hopefully this clarified things.
Let's make an example though. Let's say I create a faction called: The Empire. I join it and create my imperial army. My friend creates a faction called: The insurgency. He makes all of his insurgent npcs. Then, we go to war with each other but (what tree puncher's issue is) the insurgents are attacking my friend even though he wants to be on their same side.
So If you still want to know this, this Video might help you:
I had the same Íssue and started searching the Internet for a solution. That Video helped me a lot. But I didn't try in multiplayer yet if it really works like I want. Give it a try! Perhaps that solves your problem