We need to think WW2 bomber command.
1. Big ships stayed as close together as possible and formed interlocking fields of fire with their guns.
2. They stayed in complex formations that took considerable flying skill and discipline to maintain, often for 8 hours or more.
3. Fighters were organized in squadrons of 12 aircraft divided into 4 flights, further divided into 2-ship elements, the lead and the wingman.
We won't have 1000 heavy bombers, but we will have cargo and capital ships to protect, and they should probably fly in large groups to maximize profit and protection. We have a few big ships we can fly now, and we should practice with them. Mostly logistical stuff, like rendezvous points, formations and synchronizing quantum jumps. Fighters need to organize and train together, practicing attacking and defending the larger ships. We probably have 18 months or more to prepare...or we could just run into crap.
I have a Connie, a 'Tali, 2 Freelancers(DUR&MIS), and a bunch of fighters including a Vanguard Warden and a Sabre, that I will need to crew, and therefore I volunteer to fill positions on any ship where I am needed. I am a terrible gunner(need practice), a decent pilot and I don't think the engineer spot will be that difficult as long as we're not running back and forth between the engineer's station and a gun.