For manoeuvring, I imagine that the pilot selects an engine or group of engines and controls them with the throttle, like with a normal spacecraft. There should also be an autopilot module that, given a task containing a target altitude, orbit roundness, roll, and whatever other positioning requirements you may come up with, will use the engines you give it as it sees fit to achieve that target. Also, I imagine that in multiplayer (which I believe is necessary to KSP's commercial success) space stations will need shield modules that stop debris or craft not belonging to the owner (or owner-specified 'guests') from entering the bubble. Otherwise stations would need constant repair due to space debris and griefers.