The only thing I managed to figure out so far is to give order to attack their weapon department, with two rockers as a symbol. They seem to suggest it's possible to attack each of their weapons on their own? Maybe I am missing something.
This is the first time I reached final sector, so want to be sure I can do my best to finish this one; it's my 4th run since I started playing the game, normal from beginning.
Edit: Also, accepting any tips for the final sector.

From reading other people's posts, it seems their ships are way better equipped and/or specialized than I am; I guess it comes with experience - I've only spent couple of hours playing, so far. Playing with Torus, 4 crew members, 4 drone slots (usually Defense I and Attack I), weapons: Ion Blast II, Burst Laser I and Hull Laser II, which I switch depending on situation. All the weapons I got as loot, since I never had enough money to buy one, nor do I really know the differences much, since I tried just those I looted. Got shields upgraded to 3/4.