[Suicide Junkie]

I'm pretty sure you'll want to use some variation on mount-based QNP (quasi-newtonian propulsion).

The main point of which is that bigger ships need bigger engines to go the same speed.

The essense of mQNP is that you must use a mount in order to add engines. There will be a mount unique to each hull size, that adjusts the physical size of the engine to match the mass and profile of the ship.