Line officer side, very simple. Two roads to applying, while on active duty, and resigned. I've played on both. On active duty, complete physical, new security clearance, all the crap you had to fill out to be an officer in the first place, plus endorsement from you command to leave. Massive pain in the butt. Plus everyone in your command wondering why you want to leave their section. On civilian side, all the same crap, but I rececyled physical. However, not necessarily submitted in one package, so numerous calls to recruitor about what is needed to finish package. Plus interviews with officers about why you are fit to be a naval officer. My personal take, it is easier as a civilian, but they tell you less about what is going on.
So on the officer/ prior officer side of the house, there are a lot of monkey games you are going to face. On the enlisted side of the house, I can only imagine there are more. I hate to say it, but my seven years of experience thinks it is true. All I have to say is be extremely patient, extremely proactive. After all, I recruitor got you into this mess without full disclosure, why should it be different on the O-gang side?