As stated by Captain above, this has been something that has come up before particularly when the RP was first forming. There were a couple of RP crews that had formed around a similar time, and I was contacted by members about joining the RP Community. They however wanted to join as commissioned officer, retaining their ranks which they had used aboard their own RP crew. I refused this however, as I wanted to develop a system in which rank had to be truely earned, rather than just a title given to someone fulfilling a particular role.
A principle on which the RP Community was founded upon was that of using a proper rank system, in which all members would progress through based on a skill and ability. At this time, there are well developed criteria for each officer rank, and only when an officer fulfils those criteria can they advance. An officer must have served in their rank for a period of time before they can be advanced (you cannot be promoted to Lieutenant in week one, then promoted to Lieutenant-Commander the week after). This ensure that all higher ranking officers have extensive experience in their roles before they advance, as well as a higher set of skills and knowledge. To gain the next rank is not just a matter of "3 weeks in, your a Lieutenant now," or "you have completed 20 missions, now you have the rank of Commander," rather, you have to meet very high standards and be recognised as meeting those standards by a senior officer.
As for making a command rank (Commander and Captain ranks) and being a ship captain, the standards are even harder to meet. I expect extremely high standards of all commanding officers, includng myself (I am sure that you can get references from others online about my ability as a Captain, both inside and outside the RP Community), and feel that this standards will ensure that those in command are more than capable.
As for your own crew, it will still be possible to play together by using Academy vessels. The idea behind them was developed for this specific purpose. An Academy vessel is one used primarily for training purposes, but can also be used to play with different groups of players and in different role. Aboard an Academy vessel, any officer can take on any role in order to develop their skills. There is no official crew assigned to an Academy vessel, so anyone may join or leave when they wish. In non-RP terms, they are "free-play" ships.
TSN vessels are the "official" ships. A TSN vessel will have an assigned crew and each officer will work in a particular role. Only full officers may crew a TSN ship (Ensign and above) and only an officer holding a command rank may captain a TSN vessel. Crew will be able to apply to be assigned to a vessel (so if you don't want to serve under a particular captain, you dont have to). In non-RP terms, these ships are the "storyline" ships. They are the ones that take part in story campaigns and can develop a history of their own. They are also the ships where you can develop your own command experience and serve as a first officer in order to advance to a command role yourself (learning the ropes as it were). In terms of promotion, your actions aboard a TSN vessel are the ones that really count (actions aboard Academy vessels only really count for Officer Cadets. Of course, you can still develop other skill areas aboard Academy vessels which may also be taken in to consideration when promotions occur).
If you have any questions, then please do ask.