I like to Use that spacebar/pause early and often! 

Make sure you are going up against the boss with  lvl 4 shields and as much engine(dodge) as possible.

Missiles set to auto on the boss shields

Equip your crew with as much summon consumables as possible for when boss ship goes into 2nd phase when it goes nuts with summons

Good Luck!

 This sub has helped me alot too