I noticed their warp cores are very weak on their ships if you attack their bellys, the more damage their warp core takes, the longer it takes them to fire weapons, the slower they get, and the longer their shields can recharge. I found this is the best time to use the phased torpedos. Matans Keldon can be easily taken out but just quatanums when he's cloaked so you don't need to save them for him