If you create and save a custom race and establish your color scheme for the race, your basic ships will be the basic ships for the race you chose. From that point on you should be able to build and design ships tricked out any way you like. You will only be limited by the parts available (which will increase as the game gets closer to release).
As long as you save the game after designing your ships, they should be available for you anytime you play as that custom faction. In other words, If I build an X wing fighter as the Terrans, that ship will be in every future game that I play as the Terrans. The same should be true of any custom faction created. I can't guarantee it is working, but I can guarantee that is how it is supposed to work.
In the ship designer, pick new design. You can then pick any existing hull or just a starting cube and add parts to make it as beautiful or as goofy as you wish. If you plan to use the design with various weapon configurations, save it as a template and you can outfit it with different weapons and engines etc any time you wish. If it is njust a one time ship, fill it with weapons engines etc and save it. Templates and individual ships will be there for you each time you play as that faction
