Try to keep friendly ships in a condenced mass, more fire power on one target faster it goes down. And the sooner you take it down...the less damage gets spread to the freindly units. Try to take out the bigger or more dangerise targets first, they take more beating which is beat when the friendly are in high number and for the most part untouched. Being as the radar will be crammed with units...zooming it some will be need for targeting units around you wit clicking them on the screen, pluse it's nice for attacks of opertuneity (opens up, click fire, go back to main target). Don't fly around at max speed, your turning gets reduced..try for 1/2-3/4 for best turning.
The finel three mission I had a fully decked Sovy (didn't change much, just added a Q torp and 2 pluse phasers, beafed up what was there).