First of all we should not call single seat ships as shuttles. They can be use as a shuttle but they are not in practice. they are fighters.
I also like Donovan’s idea.
Viper’s fighters can be Venom squadron. (Victor -1…)
Raven’s might be Talon squadron. (Tango -1…)
Phoenix’s – Scarlet Squadron.(sierra -1…
Hunter’s – Claw Squadron. (Charlie-1…)
LAncer’s – Knight Squadron (Kilo -1…)
And there should be a procedure. Lets say every ship flying with 5 personel.
When the orders came to launch fighters CAptain takes helm, and weapons officers stays with him on the deck.
Helmsman, Science and engineer leaves as figher pilots.
So with captain on helm and security officer on weapons ships stays in operation actively while fighter squadrons attack to enemy at every direction.
Imagine flying with 4 full ships that makes 12 fighters in total. They have their own seperate channel. own callsigns. and ship wide call signs.
i.g. : “This is Claw Squadron leader Casanova, reading you loud and clear mothership, Claw -1 out!”