"Allows fighter or ships of up to 1000 tons to dock within the mothership."
That's the description for the Hanger technology, but it was a little hard for me to figure out the "ship" part. Heres how:
Go to the "Individual Unit Details" screen. Select a ship that will fit in the hanger: if you have 4x Hangers you can fit a 4000 ton ship. In the top right, second box down labeled Mothership(current/assigned) is a pull down box. Click the box and select your ship.
Now I can reload my box launchers with an auxiliary hanger ship. Missiles away!