I try and use my team's free airspace in our deepbase to organize my bombers. Here's some random tips:
Fully re-armed/repaired aircraft will take off an airpad and fly to the airpad's waypoint. You can set factory and airpad waypoints to group all things that take off from those airpads,
Selecting a large group of bombers and clicking the 'repair and rerm' button in the UI will only give orders to damaged or unarmed bombers. You can set a move order and then press the button to sift out all but the ready and full HP bombers in a selection.
Give move orders after attack commands and bombers will turn towards that order instead of the nearest airpad after dropping payload. This makes for fluid turns away from AA every time.
if secureing a kill with very many bomers, use the move order trick to not have bombers flying out and circleing in the middle of the battlefield. Bombers that lose the attack comand due to the unit dieing before the bomb drops will fly aimlessly into AA.
Think about using linemove in interesting ways to group and then distribute bombers to be concentrated and also not too vulnerable to AOE.