You need a launching bay on your main ship in order to use space-borne ships. After you purchase ships for your bay, simply cycle through your secondary weapons until it lists the ships you want to launch. You can then fire the space-borne ships like you would any other weapon. Option Recall (default - c) recalls them back to your ship's bay. This can be used strategically since space-borne ships get instantly repaired and rearmed when recalled.