better engine control mod??

[CCIP]

Not possible as far as I'm aware since it's a hard-coded feature. Instead of separate engines, in the data files every sub is just assigned a general thrust power (for diesels and electrics); and where that power actually comes from on the sub is irrelevant for the game's physics engine - it's just an abstract force that pushes your boat along. So there's really no way to separate the engines with a mod.