I'm suggesting you couldn't, but if you insisted (I confess not being familiar with HMA)
1) Build your compact-core "JumpShip" with the SI needed to support the drives you want it to have eventually
2) Allocate accommodation, basic life support, station-keeping drives and a few docking collars.
3) Call everything else "cargo", but basically leave it as empty space.
What you'll have is a thick, lumpy looking JumpShip.
Now you have to go house rules. Assume everything else you want (guns, fuel, fighter bays, armour) comes in bolt-on modules made somewhere else. Impose a penalty of (say) 10% representing general inefficiencies. So if you wanted to add a 10,000 ton fighter bay, it weighs 11,000 tons; 200 tons of armour uses up 220 tons of "cargo space", etc.
Does that make sense?
W.