When you finish building a new ship, load it with the weapons (Plasma Beam for both weapons is recommended). When it is fully charged and ready for flight, transfer it to another base. When it gets to the base, immediately send it out on patrol. Click the ship and you will see that its fuel is 0%. That means it will not run out of fuel. Make sure that when you send the ship out on patrol, send it to the opposite side of the planet or a long way from your base. This allows you to catch the ship after it attacks the enemy before it can return to base. This is best done with the FireStorm craft. They are cheap and quick to build. The firepower is just as good as the Avenger, which cost lots more and takes longer to build.
Information in this section was contributed by TheRaven.