I was playing a Star Trek mod called "The Trek Wars"
http://www.moddb.com/mods/trek-wars-revival which is the only Star Trek mod that I know of that has the Dominion (other than Galaxy at War, but I couldn't install that one no matter what). The Jem'Hadar's Phased-Polaron Beams don't skip shields like they're supposed to, a criticism that I and many other people made since the Consortium has mass drivers and is OP as all hell, and the Rebels and Empire have proton torpedoes on their bombers and ships which also ignore shields.
Are there files I can go into to make the Dominion's phased polaron beams skip shields too?
Solved: I thank DragonNation5523 for letting me in on what I need to do; go into Projectiles.xml and change "Projectile_Does_Shield_Damage" from "Yes" to "No".