I have a beam boat also but I'm a tactical officer.. What I do is cycle my weapon buffs to keep reasonable DPS and make extensive use of weapon batteries. For instance in KASE I usually keep gard on probe and I rarely have any that goes beyond me, I always park above the travel lane just behond the range of the gate (10-10.5 km). One trick I use is hit weapon batteries or any buff than use fire at will. By the time the first on blow up the second one (and more if there is) already has his shield down and close to 50% hull.
When I need to kill something real fast I stack up my tac buff for a good burst of power. Now my tactical officer has almost all weapons skill maxed out so that help a lot.
Also I don't use beam overload anymore, always get weapon power to zero and it always take a while before I do decent damage again if no buff or batteries are availlable. I use 8 beams and power level usually go to around 50 to 60% at the end of each cycle and never below 85% on batteries. One thing I like about antiproton is that you get lots of criticals hits so that helps keep DPS up.
I almost always have weapon power set to 100%, plus any buff from console and stuff on top (120% now). Also to maximize batteries I have two purple maintenance engineer which gives me 4 second extra on batteries (my skill are maxed out also for batteries).