Check in the ability's file, there should be a line that says "Buffisstackable TRUE" and then there should be another one not far from it stating the number of stacks, if you just change the first line the other is still set to 0 or 1 by default so you have to give it a max number, See the advent turret's ability for synergy, that one's stackable by 3 on the vanilla game.

yes, I have changed the stacking limit and it doesn't give me the variable bonus I want because it automatically gives it the max bonus. I want the bonus to change based on how many friendly ships are in orbit