Buoyancy can be either positive, negative, or neutral. If something is positively buoyant, it floats. If it is negatively buoyant, it sinks to the bottom.
Neutral buoyancy is when life gets interesting and is vital to understanding submarines. As an object sinks, it may reach a point where its negative and positive buoyancy balance out and the object becomes neutrally buoyant. In other words, it will sink no further, nor will it float any higher.
So if you want to sail your submarine at a depth of 100 feet, you add extra sea water and vent air until you add enough weight to sink 100 feet but no more. At that point, adding more water and the boat sinks lower. Adding more air and the boat rises.
A submarine is designed with an inner, pressure hull and an outer hull. Water is added in the space between the inner and outer hull when the submarine wants to submerge. The pressure hull is only external in a few select locations.
Even if a submarine is sitting on the bottom and unable to get off the bottom, the inner pressure hull can still be dry, providing this has occurred above the boat's crush depth. Only way I can think of to know whether a submarine is flooded is if one of the hatches is open or there is structural damage. If the pressure hull is intact, it is unlikely that the inner hull will be flooded. Although amazingly complex, the principles for submarines are relatively straight-forward, and you'd need to present me with a very good reason for why the inner, pressure hull is flooded.
Remember that the pressure hull is designed to reach depths of a thousand feet or so, where the pressure is over 400 pounds per square inch.
Jim Clark-Dawe