From the hangar view, you can fully customize every aspect of your ship designs.
By default, your ship will be outfitted with nothing but surplus components.
Even early on, you'll have access to several different components.
Click on the mount icons on the ship to see what else you can install.
You can also modify shields, engines and the reactor, which powers everything on the ship.
The more advanced the component, the more it will cost you.
Be sure to refit your obsolete ships whenever you unlock new technology.
As your mothership becomes more advanced, additional hangars will be added.
Old hangars will also be upgraded, allowing them to support larger ships.
It's usually wise to build the largest ships available if you can afford them.