In my opinion the game designers understood submarine operation about as well as the average Aroma Therapist does.
The way it worked in reality is they would make a daily trim dive, leveling at 100 feet and slowing down, pumping fore-aft in-out until they had the boat balanced and as close to NEUTRAL buoyancy as they could get. Then they would set a pointer on the negative tank gauge for the amount of water it held at neutral buoyancy.
When diving all the tanks were flooded for negative buoyancy to get under in a hurry, then before getting too deep the order came "BLOW NEGATIVE TO THE MARK". The negative tank blown to the previous mark gave the sub approximately the same neutral buoyancy from the most recent trim dive, the depth was then adjusted DYNAMICALLY with the diving planes to go up or down or hold depth.
In real life unlike the game you couldn't stop motors and go dead in the water (zero knots) and be able to hold a steady depth or even stay level fore and aft, since perfect neutral buoyancy is nearly impossible. So they maintained a minimum speed of 2 knots at all times while submerged, changed or held depth only with the diving planes and never fiddled with ballast at all unless something happened to change the balance or neutral buoyancy. When they surfaced they blew air into the tanks to get positive buoyancy, and also used the diving planes to go up. But for going from 100 feet down to 300 feet or rising from 300 feet to periscope depth it was diving planes only, never touching the ballast controls.