Mr_yourface13 I have already. Using my phone right now to post but if you go to ship designs and view my Executor SSD or the Battlestar Theseus both have isolated compartments that include:
Various weapons
A cockpit
At least 1 reactor
At least 1 ammo factory per gun
Crew (as per how much is needed).
Ammo and power storage.
Shields (if required)
Another thing I like to do is place a cannon with 1 layer of armour behind it then a ammo factory. Forces the crew to take it directly to the gun rather then fill up every storage on the entire ship.
If you have ABH's mod you can place a mini fusion reactor next to a object that requires power and the crew will take it directly to the engine, weapon, etc.
Also don't worry about placing ammo near your guns, as long as the gun has armour behind it, it should stop a cannon round. If it gets penetrated your already dead. It's an all or nothing armour scheme that works extremely well especially on large battleships.
You can also take a look at my Aegis CCG, my latest modification to a ship. I modified one of @AdmiralRodriguez designs using isolated compartments and all or nothing armour and now it works much better (at least for my needs).
