I'm new to GalCiv2 and the ship design stuff wasn't well explained in the tutorial. The game provides a number of basic ship designs as you discover new basic techs, but will those designs be automatically upgraded to the highest quality parts of each type as you discover new parts?
Nope. You have to go and upgrade these manually through the shipyard. Usually the prebuilt ship designs are just helpers to get you started. Some designs are unlocked if you research certain tech levels. Once you get familiar with the game you should be constantly updating your ship designs with the latest components as you progress through the tech tree. It is mostly advisable to build your own designs instead of relying on the prebuilt ones.