I haven't built any in a while, but this is how I do it, I place 2 sets of ballast tanks, on 2 switches, and turn on one of the sets, this will be our main-floating ballast. Then i submerge it in the water, and keep adding weight or removing buoyant objects to make it float more or less until it is neutrally buoyant I.E floating still, No movement upwards or downwards, So if you turn switch 1 off, It floats nicely, But if you turn it on, It becomes neutrally buoyant, Then, I take the second ballast set and put that to another switch, So you can turn both ballast tanks on to sink, both off to float, and the first one on to be neutrally buoyant!

I havent built submarines in a while, but this is usually how i do it.