This likely has an obvious answer, but once I took the ion-bolt module off the flagship I was never able to put it back on. Even after buying information on improved weapons from the traders I can't arm the main ship. I'm sure I'm just missing something from the interface so if someone would point me in the right direction...
only those slots marked with blue frame can occupy weapons. Also the slot in which you put the weapon determines the direction of the shot, i.e putting it in the back of the ship will make the cannon fire backwards, the front will make it fire straight, and the rest do the sides. you'll figure it out.