Not a popular topic I see!

I decided to use the Warp Rift rules for now, with the ships dispersed through my fleets as such:
IMPERIAL NAVY FLEETEmperor Battleship (Cruiser)
Tyrant Battleship (Cruiser) x2
Thunderbolt Cruiser (Corvette) x6
Constellation Targeting Ships x6
ROGUE TRADER FLEETIronclad Battleship (Cruiser) x2
Gothic Battleship (Cruiser)
Castellan Shield Ship
Galaxy Troopship
Goliath Factory Ship
Cobra Destroyers x8
DEFENSE FLEETStalwart Escort x5
My reasons for this arrangement are based on a combination of the function of the ship and the hull style.
For example The Gothic ship style (including the smaller Ironclad and Cobra) have an exotic feel that I thought fit better with the Rogue Trader fleet. As did the shield, troop, and factory ships for reasons of function. The Stalwart was described as a non-warp/in-system ship, so I included it with my "Defense" fleet. Everything else went with the Imperials.