Just to clarify on neXib's post;
When you dock at a station, go to Station Services. Then, choose 'Shipyard' from the list. In the window it brings up, to the far right there will be a tab saying "Ship Locations" or similar. Choose this, and it will tell you in what system the Eagle is located.
You must then go to that system in the Galaxy Map, and go to its System View. Over one of the Starport icons will be a icon of a ship (in blue I think). If you then fly to and dock at that station, in the Shipyard you will be able to choose to use the Eagle.