I'm supposed to wear the AF "senior" pilot wings over the Naval Aviator wings. The gold wing mafia is pretty strong here (and across the state) so it's largely left up to the individual preference on most occasions. Command billets and above all wear the AF wings on top. My name patches all have my gold wings on top. I've worn my blues exactly once in 4 years, and I was/am brainwashed by the USMC, so I matched the Sr gold wing guy and wore the AF wings on top.
The AF does have RPA/drone pilot specific wings (as does the USMC) for the folks who went through the undergraduate RPA training course, but anyone who goes through traditional pilot training wears the traditional pilot wings.