You need a launching bay on your main ship in order to use space-borne ships. After you have 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. Recall (default - option c) them back to your ship's bay. This can be used strategically since space-borne ships get instantly repaired and rearmed when recalled.