They use a few main ways to communicate- radios (not too different from what combat controllers use so the grunts can talk to airplanes... since you said you're USAF) both line of sight and satellite com, usually encrypted (but partner nation ships don't have our crypto if that's part of your story), MIRC chat started being a thing about 20 years ago and there was a big debate about ten years ago whether it was appropriate for kill orders. The old NATO data link systems were very labor intensive and the console operators on each ship had to be able to communicate with each other to manage all those different tracks (friendly, enemy, and neutral contacts in the air, on the surface, and subsurface). Datalink stuff is a lot more automated nowadays though.
If your story involves GPS not working then accurately tracking all the friendlies and bad guys gets more complicated. Each friendly ship's tactical plot is offset from the others by some margin of error. Dealing with that is kind of a lost art. If you want your subordinate ships to engage several enemy targets then coordination that can be complicated. The old Soviet doctrine was to shoot a crap ton of huge missiles and let the laws of probability sort it out. That was a pretty good doctrine for a WW3 scenario but not really appropriate for a limited war or a regional war scenario. Western doctrine, as far engagements that were not all-out war, has always been afraid of one of our anti ship missiles hitting the wrong target. What that means is you need really good targeting data before launching one- which means good comms and an accurate picture of everything else that is going on anywhere close to the bad guy you're going to shoot with the missile.
Just some ideas and broad, qualitative concepts for you. I think
@AllAmerican75 will probably give you more useful gouge.
