Yes, you need to be in the room labelled "Cockpit" of your ship that is assigned to you a commander and as pilot.
Next follow what is in "The Guide" (will repost here as well)
To move from place-to-place in space, you need to do the following:
1. Find the cockpit link, (under ::Control:: on the sidebar)
2. In the middle of the webpage, you should see a Travel button. Press it.
3. On the bottom half of the screen, some other buttons should appear. Click on either sublight or hyperspace.
4. Choose the coordinates and speed you desire, then press the Go button.
But I strongly suggest you find a faction mate that will help you out with any further questions.