Skytrex do mix with Navwar, but make sure you buy all ships of a given class from one or the other.
For collecting ships, I’d suggest pick a battle that interests you (preferably a fairly balanced one), and get all the ships for that battle.
Are you more interested in North Atlantic or the Med?
Barents Sea is an interesting battle with a good mix of forces.
You may as well get all the German capital ships because there aren’t very many of them.
You’ll also need about a dozen destroyers for the Germans.