I'm playing the TEAM path.

First of all, you should know that you can't operate all of the
controls until you get rid of Sophia's guard.

There are four controls.  Two require puzzle solving to reach.

For example, you need to unlock the rudder control.

You'll have that key once you find the stones.  See another question for
more details.

To fix the depth lever, you need to find a replacement stick.

There's no real logic to finding the part.  Try anything that makes sense.

Use the plunger from next to the Nazi guard.

Now you should be able to find all four controls.  There are two in the
aft section (reverse, speed) and two near the sub's center (depth, rudder).

There is an entrance to Atlantis on the left side of the screen.

You need to change your depth, direction, and position (back or front of
the screen) to get to it.

You will have to stop the sub to change the direction, and can't turn
while you're in reverse.