I like the idea of having a ship docked as a QRF, whilst the others power down properly in the shipyards. On a scramble, the QRF move out first, followed by the other ships when we have shuttle across to them, should they be required of course.
I agree that the command staff of the station should be in charge on a station. At the same time, we need to be able to deploy when required. I think therefore, whomever is in charge of the division at the time should hold the same level of position as the station commander. In a way, the station is there so that we as ship personnel can do our job. I think therefore that, if a QRF was to be launched, the station commander would have to know about it and possibly even be the one to authorise it. Once out of dock though, we are in control of the situation.
In terms of how it runs on a station, the station commander could appoint an officer of the watch; someone who sits on the command deck and keeps things running smoothly. Any emergencies, the station commander would be alerted, but most other things would be dealt with by the officer of the watch.
If the division needs to launch, we need to first inform the station commander. He would likely already be aware of the orders. The station commander would then facilitate our launch.
As for marines, like the way our ships and crews work, they should report their activities to the station commander and work with them. The commanding officer of the marines would be below the station commander and division commander in terms of chain of command though, answering to the needs of both.