Rollin', Rollin', Rollin'...
So. You've built your sub, ballasted it perfectly to sit at the correct waterline in both surfaced and submerged trim, taken it out on the water and...
...it rolls on its side like some sort of sick whale when you try to accelerate.
Frustrated at the silly-looking operation of the boat, you decide to ignore it, only to find that the boat wants to dive when you turn left or right and keeping track of the boat when you're submerged is like high school algebra, only algebra was easier and significantly less expensive when you got something wrong.
So what's up?
What is occurring is a very common issue with modern nuclear boat models with a single, large propeller. The phenomenon is best known as "torque-induced roll" and is basically a result of your motor trying to turn the prop and the prop biting into the (mostly)stationary water around it. The result, just like if you snag a drill bit in wood, is that the boat wants to spin about the prop shaft, and in this case leans off to one side, opposite of the direction of the spinning propeller.
Okay... so what's the fix?
The solution is to increase the boat's tendency to sit upright in the water, making it more statically stable. Your prop is introducing a rolling moment to the boat's hull (to speak in engineering terms). You need to bump up your righting moment by increasing the difference between your foam's ability to lift the boat and your ballast's ability to sink it. The bigger the difference, the more stable your boat is.
To put it more simply, imagine you have the boat pictured at right. It's foam creates a force that wants to lift the boat and it's ballast creates one that wants to pull it downward. If you have very little force acting on each of those spots, you'll be able to roll the boat very easily. The more force you put on the two points in opposite directions, the harder it will be roll the boat about.
So, what you need to do is add foam just below your surfaced waterline and add ballast to the sub as low down in the bottom of the keel as you can get it.
If you don't want to upset your carefully balanced trim, you can use a simple process to ensure that each of the two forces you're creating cancel each other out, leaving your boat's overall trim unchanged.
Find out how much additional foam you can add. Cut the pieces, place them in the hull, but don't attach them yet.
Now that you've figured out the maximum amount of flotation you'll be adding, simply bundle your foam pieces together with an elastic band and add some ballast weights under the elastic until your crude little raft just barely floats.
Add the foam to your model. Add the ballast to your model. Play with placement a bit until your forward/stern trim is right, then secure everything in place.
You're done! You'll never completely get rid of that roll, but you can reduce it significantly with this simple process.