[Echo76]

After you complete the goals for the mission you picked, return to your port and end patrol, Your home port shows in the map as blue icon with a white sub in center of it. You can end the patrol anytime you wish but don't do it unless your boats hull is badly damaged as the missions have a timeline and ending the patrol takes a few weeks before you're ready to sail again.

If you run out of torps before you have completed your objective, you can stop in any friendly port and replenish your ammo / fuel and continue with your mission. Refitting is instant. I hope this helps.

P.S. Complete a few missions and you will get the opportunity get a new sub upon arriving your home port.