I usually use Trebucets and Mortars when defending my settlements as a counter-siege equipment force. I try to take out their towers or their Artillery.

Ballistae I sometimes use for domestic field battles (When an enemy enters my territory.
But generally I hate to use Artillery for my invasion armies (unless they land by sea, or are taking on a CITADEL) because of the negative effect on Marching Distances - i hate that shit lol