Saving your custom ship designs as templates is necessary to be able to select those ships from the lists in the civ builder fleet tab. Unless saved as template they will not show in selection of ship designs to choose from for each class and hull size.
Templates themselves do not have weapons or defenses. After the ship set is created and saved the game automatically applies weapons and defenses based on class and ship roles and are available to build from shipyards. Larger hull ships in the ship set become available after you complete the research unlocking them.