Verify the damage screen of your sub and wait until the critical repairs are done, but do not use TC higher than 16.
If you see red zone damages with less than 20% status, then assume it's destroyed and cannot be repaired. Other things can only be repaired when surfaced. Read description.
If you don't have compressed air left, then that's too bad if you are too deep and cannot emerge normally because too many destroyed components, RIP...Use the gramophone until batteries run out, or use the command 'all crew on the bridge'
Otherwise use the command Blow All Ballasts once repairs are done, you can do this only once, so chose the right moment...
Everytime your sub gets damaged and you are underwater, don't use TC>16.
With TC>16 this will increase the damages , so you are in the situation you are now.
Disable Battlestations and command your chief engineer to accelerate the repairs, you can do that 1 time every 2 hours I think. Revert this command once repairs are done, else your crew will not perform well elsewhere.