Not to seem dense here but how do you equip weapons from the super weapons that you build?

I think you mean the nanoweapons. Once you have them built go to your Heroes screen and tap on any 5 star hero. They will have a small box on their screen to the right which you can tap to enter the weapon select screen.

If the box has a + in it then you can select a weapon. If your hero is below level 211 then it will show a lock and you cannot apply a weapon until you reach level 211 on that hero.