For new fighter types you need the FighterRACEname.enity and the SquadRACEname.entity as you said. In Entrenchment/Diplomacy you must then add these two files to the entity.manifest (that is basically a list of all .entity files the game should be allowed to use when running the mod) Afaik there is no reference to the SC in the player file.
Then you must add the Squad entity to a carrier ship. Any ship can have at most 4 different kinds of strike craft. (As of Diplomacy, I don't know the limit in Vanilla/Entrenchment) You can set different kinds of SC for different carrier ships.
So you can't have an SD with TIE Fighter/Bomber/Interceptor/Defender variants and Gunboats, but you can put all 4 TIEs on 1 ship, and the Gunboats+2 TIEs on another.
There is no limit to the number of Squads a ship can hold btw, apart from what your PC can manage.
And from my experience putting shields on SC crashes the game the moment they're attacked, so if you have shielded SC be careful, and you might have to remove the shields.