Few Questions.
How does One store a Ship of 500-1K? How do they transit a Warp Point? Can they Fit Into a Hanger? if not How does one Reload the Box Launchers? Refueling? Repairs? Crew Transfers?
Is there a Ship that is Capable of Doing any to All of these?
It is Possible that there are answers somewhere else if so please Direct me!
Storage:
Hangars/Boat bays really don't care about the size of ship you put in them, so long as it fits.
As to how to store them, you can use all but one of the methods that fighters can use.
With the FACs in a different task group (not certain in possible if in same) as the target carrier:
Select the FAC TG.
Show Task Groups in the system location list.
Under available actions there should be "Land on specified Mothership". with 'sub options' for assigning to that carrier or not.
Select the Carrier you want them to land on in the 'Select Mothership' box.
Click 'Add Move'. (No double clicking allowed due to the select Mothership part)
And now they work mostly like fighters, just being unable to use the squadron functions. I believe there is another way to manage this, but I do not personally know how.
As to the rest of your questions, I think this answers them? (In a round-a-bout way)
