Dogscoff is correct. You can also give the second design a new tech requirement, adding a technology to the tech.txt file and giving it a starting value of 1. That means when you start the game its already researched. Then put all of your new weapons for it under that technology. For example:
Big Ship Technology
Level I Gives you Big Ship Hull
Level I Big Ship Weapons Technology
Big Ship Weapons Technology
Level I Big Gun A
Level II Big Bun B
etc.
If you opt for Dogscoffs idea and go with mounts, simply make the component 10,000kt and give it a specific weap family number. When you create the mount, set the mount size min/max to the size of the HULL you want it to work with and us the weapon or component number fir tge 10,000kt comp or weap that you wish.
For examples, look to the Star Trek Mod, Federation Cloaking Technology, Federation or is it Defiant Cloaking in the mounts and components files.
Good luck.
Also there is a lot of information over at the Mod Works on
www.spaceempires.net/home in the forums.