I would recommend you get a copy of 'Model Submarine technology' by Norbert Bruggen from Traplet. It's a tough read, but covers all the basic principles of making sound watertight enclosures, including best practice for sealing and construction. Ballast system are covered in a great deal of detail, as well as trim and auxiliary systems.
The electronics in the book are somewhat dates, and these days it's a lot easier and less expensive to purchase these items commercially.
A lathe makes things much easier when it comes to constructing endcaps, glanded shafts etc. However it's not essential.
I would recommend you purchase a commercial shaft seal from Sub tech. These are special low friction seals, design to prevent the ingress of water, and are reasonably price. Some people get by with a grease filled propshaft, and it works, but the shaft seal is better.
I would personally recommend you start off by constructing a dynamic diver. When you are confident with building a watertight enclosure, trimming a boat out, then you can add a ballast system. I would also recommend you build a cylindrical watertight enclosure rather than a box. Although the latter can work well enough, there is far more room for error IMO.
Experience with helicopters will serve you well. In many respects model submarines have far more in common with flying machines than surface craft. The same basic principles apply, you are just 'flying' through a much denser fluid, which is good deal less forgiving than air.
Just like a model heli, placement of centre of gravity is critical, and you should replace the centre of lift, with the centre of buoyancy, the force acting up on our submarines.
For the sub to have a level trim, these two forces must aligned vertically. The greater the height between these two forces, the more stable the boat is.
In other words, keep the heavy things low in the boat.
