When a sub dives to a certain depth, is that depth
measured from the bottom of the sub, the middle,
or the top. In other words, if it dives to 200 feet,
does that mean there is 200 feet of water above
it or that the bottom of it is 200 feet below the
surface?

Normally "depth to keel.

I don't know squat diddly about submarines, but I think I can answer this
question. *If* the dive indicator reads "zero" when the sub is on the surface,
the submerged depth would be measured from the normally ballasted waterline to
the surface. It wouldn't seem logical, otherwise.