Overall there was no segregation between Luftwaffe and Wehrmacht soldiers, as for naval units, I do know that some camps in the United States were majority naval troops such as Camp Papago Park.

Generally speaking there was no overall need to segregate the soldiers as the the Luftwaffe personnel certainly wouldn't be getting near any aircraft. In accordance with the Geneva Conventions, German POWs in the U.S. lived a pretty good life. They planted gardens, ate decently, and occasionally were even allowed to go out on the town to go watch movies. They were contracted out to work with farmers, non-war related factories, and in the case of Camp Clinton in Mississippi, even build The Mississippi River Basin Model, which was used to conduct flood control testing.

Hard core Nazis were generally segregated from regular troops and housed in places like the POW camp in Alva, Oklahoma which was called Nazilager. Both hard core Nazis as well as the others were still subject to "re-education" by anti-Nazi prisoners and propaganda films and newsreeels, especially after the liberation of the concentration camps. They were forced to watch films documenting the atrocities of the camps and often there were mixed feelings, some refusing to believe, some becoming enraged at 'the lies', and some weeping openly.