It helps (me at least
if you mentall separate your ships into 6 categories:
Slow, Weak vs. Fighters: Cruisers
Fast, Weak vs. Fighters: Deflectors, Anti-Armor
Slow, Weak vs. Bombers: MLRS
Fast, Weak vs. Bombers: Fighters
Slow, Weak vs. Cruisers: Munitions
Fast, Weak vs. Cruisers: Bombers
(18 speed is my personal cutoff for slow/fast)
Every ship should fall into one of these categories... Then, plan your movements like Velox suggested...
If you don't want to goto that trouble, I found that the a good "lazy" way to do it is just send my bombers in second... This will eliminate a good portion of your "stupid" losses