I'm really struggling with the BoP right now, too. I just unlocked Klingon a few days ago and I'm still trying to figure out how to handle the BoP. This thread has been quite helpful. Actually I thought I was doing pretty well until the "All Around the Mulberry Bush" mission. I got killed three times before I was able to finish it. Ugh.
I'm wondering, though, if I'm approaching it the wrong way. Because the BoP is so squishy I decided to use two engineer BOFFS (I'm Tactical) to help keep myself alive. But should I go for two tactical BOFFS to try to increase my offensive strength and focus on killing before being killed?