That´s what the "join" command (TG window) is for. I usually would have all three squadron in one TG, then I split two squadrons (again TG window, 2nd tab "special orders", select the ships of a squadron and hit "split TG")
Select the main TG again and do the same for the second squadron.
If the main TG was named, Battlefleet, for example, you will now have
Battlefleet
Battlefleet #2
and Battlefleet #3
After transiting, give Battlefleet #2 and #3 the command to joint Battlefleet.
The splitting off can be easier, if you have organized your TG on the "Naval Organisation" tab (same window)
Select the Squadron and hit "Branch Only" (or "Branch+sub", depending on your organisation)
Fighters:
I don´t think of them as a very early tech, but they aren´t a late game tech either. Personally, I usually go for it between development of Ion-engines and Magneto-Plasma drives (this varies a bit, of course)
It helps that I go for launcher size reduction 25% anyway pretty early, so box launchers are only one tech-level away.
Prefab PDCs. Yes, you need a little minerals, I usually put a couple hundred of all minerals in the cargo hold along with the PDC parts.