Simply giving the enclave starship a build-loop with drones and an FRD-move order to the point where you want the drones to "base" from should suffice for them to fight effectively. They'll autotarget (mostly by picking up the target list of a nearby drone of the same type and mark) and fire away.
I wouldn't suggest trying to take out kiting units (raptor, bombard, sniper, etc) with drones unless you can sandwich them somehow.
If you really want the drones under manual control on a number, assign that number to the enclave and all units it produces should have that number when they come out.