There is always a "fleet" area that you have to run through to get back to your ship. Usually you access this fleet area by clicking on the door of what looks like a ship and selecting "Drummond Kaas Fleet" or whatever looks similar to that. It will take you to a big building where you need to find the elevator up to your classes ship dock.

Each elevator in the building is labeled as to which classes ship it goes to, so just go to the map and hover over the elevators till you find the one labeled for your class.

Hope that helps, sorta hard to explain.