The cutters wouldn't fit in the empty weapons bays, since there is 50% wastage when using empty weapons bays for storing small craft. The design I described above converts the two unused Gunnery Decks into something else, anyway.
I think Hans is imagining that the cutters will use a 50-ton version of the same "racetrack" system the fighters use. You could imagine cutters moving around on this, with "sidings" for storing the various cutter modules (perhaps in some kind of "rotary magazine" several decks high?) and for cutter maintenance.
As for what kind of cutter modules, adding two more cutters and 5 extra modules still leaves 667 dtons of "unused space" to show the effect of the conversion (and give the middies someplace to play games that the instructors shouldn't know about....) So you'd have 15 cutter modules.
I'd carry 4 passenger/cargo modules, 1 "captain's yacht" module, a fuel skimmer, two assault modules, a boarding module, two fighter modules, a sensor/ECM module, a weapons module, an ATV module, and a deployable base module. That should let you cover a pretty wide range of training missions, and you could always pick up some extras from a friendly naval base if you had something special in mind.
Wartime modules would depend on the assigned mission. With her high jump capacity, this ship would probably be part of a "quick-reaction" force, or be assigned to raiding behind enemy lines. Either way her module loadout would depend on her mission. Note that if she doesn't carry the middies she can carry lots of extra troops.
On the deckplans, I notice that the Captain's and XO's suites are duplicated on the Auxiliary Bridge deck. I would think that those duplicate suites would become the quarters and offices of the Academy officers responsible for training the middies, probably including that RADM Count Whoever He Is in charge of this flying grade school.
