Decide what will be your prime target 1st & then pick weapons to suit defeating your victim.
So assuming Transports - Experiment with set ups - The Codes do more damage than civ weapons, but are very hungry on your energy.
Learn to set up Weapon Groups - (1) All guns blazing (2) Hull Busters only (3) Shield removal - 2 debs + how many Hull Busters you can fire where energy drain is minimal.
Without assistance a 100k shield is going to be slow to remove with 2 debs & 5 hull busters.
Screamer mines spammed off are brutal on low agile ships.
Nukes are multi purpose & are more effective on fighters.
A Cruise Disruptor is must - I'd recommend a Train.
A CD allows you to isolate the enemy ship & being kicked out of cruise is very demoralising as a Transport Pilot.
If you are going to team up, then a MR on a sister ship becomes viable.
A final tip on Energy Management - you regain Energy quicker when in Engine Kill, than mouse flight