FYI, automated shipyards are a losing proposition right now, but what you can do is make make factories designed to manufacture and pull the exact number of resources needed to fill a BP and drop them all on 1 box. If you want to mass produce drones, you then make what is called a drone rack, where you create a basic wireframe with some rails on it and a logic driven auto launcher (racks are typically have 4-24 drones each). Then you dock your drones to it and BP it. So if you want a highly automated way to make a fleet of drones, you use auto factories to produce the raw materials, then you cram them into a rack BP so you can spawn several at a time.
This is also good if you want preset fleet proportions, for example (6 interceptors, 4 bombers, & 1 E-War command frigate) per rack.
Some racks even use warheads to make self destruct triggers that overheat the rack after launching the drones so you don't have any permanent space junk.