To finish a patrol get within 30 km of a friendly base and hit escape. choose exit patrol. When you do that you should be given an option of either to continue with the patrol or Dock at XXXX (what port your near). If the option doesn't appear, then your not close enough to the port yet. Try to make it back to the port your ordered too, you get more renown this way.
With saving your game, don't save while your underwater, it tends to crash the game when you reload. Don't add any mods to the game or any tweaks untill you're back in port as that can cause a CTD.
Best of luck!
