Basically, you have the sailing crew, and the combat company, which early on, would have consisted of archers and marines. Simplistically, the Crown authorizes an aristocrat, or a professional soldier, to raise a company of fighting men, and since that fighting will happen on water, the requisite vessel and crew are add ons.
I think that flag officers are now required to have a Masters or Doctorate in some related field, like International Relations, plus undergoing Staff and/or Command Schools.