(Instructions from mid-OB, haven't gotten a new ship since then)
Go back to the shipyard, find the center console thing (With the big holographic ship). Between that and the counter where you can buy low level equipment are two screens, one on the left and one on the right (looking at the counter). Left is the ship customizer guy you went to when you wanted to customize your miranda (assuming you didn't use the other guy). The right screen is the guy who will let you choose your ship, go to him, select your new ship and hit the button at the bottom. Enjoy.
In step-by-step format:
1. Go to the shipyard (at starbase)
2. Find the guy who lets you change ships (he's by a tall screen)
3. Select your new ship
4. Hit the button at the bottom