The clean way to do it, would be to go to module_scripts, and install special cases for your factions there. The relevant ones should be:
"decide_faction_ai"
"npc_decision_checklist_peace_or_war"
Both scripts are horrible, horrible spaghetti code, so good luck with that.
Alternatively, you could try some dirty hacks, like a simple trigger that constantly increases or decreases relations between factions and rulers. Also, "game_start" contains a few lines that make one faction claim anothers' centers. Removing contested claims tends to make them more peaceful, adding more makes them hate each others guts.