The Modular Sub System (MSS) Overview
I have a detailed video overview of this system on my YouTube channel. Feel free to take a look here. There is a lot of additional information that I included in the video, so I do urge you to take a look!
One of the challenges with large RC submarines is the creation of a control and command system that can handle propulsion, control and buoyancy in such a large scale.

Historically, most builders will pursue what is called the "dry hull method". In this setup, a large portion of the boat is sectioned off as a completely dry section and the electronic components are housed within in. The advantage is that this results in a huge amount of open volume to install components, allowing for easy installation and access. The downside, however, is that sealing the very large lids for these sections is problematic and often time-consuming to gain access to and seal up again. Additionally, the creation of such a large sealed volume means that these boats have a tremendous amount of buoyancy which needs to be offset by the installation of copious amounts of fixed ballast. This results in tremendously heavy models that are difficult to transport, launch and retrieve.
Watertight cylinders are the traditional alternative to dry hull boats, however they don't lend themselves well to large scale submarines. Sealing very large diameter tubes reliably and in a manner that is easy to access is challenging, as is housing the larger batteries and components required by much larger models.
An alternative to these two construction methodologies is something that I call the "Modular Sub System" or MSS for short. My version of this system was inspired by a gentleman by the name of Ed Tordahl, who constructed a large-scale 1:48 USS Skipjack model using a variation of this method.
I took his experience, added in my own, and came up with the following solution.
MSS Overview

The idea behind the MSS is utilizing a series of segregated, modular watertight compartments, each one grouped by function and/or location in the boat. Making these sub-sections modular and separate allows for installation in the most advantageous location in the boat, keeps damage caused by watertight integrity failure limited, and allows for much easier maintenance and upgrading at later times.
In my preliminary project, the system is composed of three primary modules, however there is no theoretical limit to the number that you can employ, depending on your model and what you're trying to achieve. Each main module is built from a high-strength polycarbonate waterproof case. These cases are completely waterproof, tested in excess of 80ft depth out-of-the-box. Module penetrations such as linkages and drive shafts are installed by drilling holes in the thick walls of the case and installing high-quality cup seals to seal the shaft. Access to the interior of the modules is gained by simply flipping open two latches and opening the lid. This is much different than the traditional dry hull boats that use dozens (and dozens) of nuts to hold down the lid.

1.) Stern Drive Module: This module houses the radio receiver, the main drive motor, the motor ESC and two servos, one for rudder and one for the stern dive planes.
Receiver: My radio system of choice in this case was the excellent VEX 6-channel package, available for purchase at the Nautilus Drydocks (www.nautilusdrydocks.com)
Main Drive Motor: This was the blower motor from a vehicle's air conditioning system, purchased at a surplus store. It is approximately 3" in diameter, run direct-drive to the main propeller. It is high-efficiency with internal noise suppression, turning at approximately 5,000rpm.
ESC: I utilized the Mtroniks SUB10, 40A ESC with integrated BEC
Servos: I used standard Futaba S3004 servos