Hi and welcome to the forums
When you are at the subpen you can talk to 2 officers there.
They both stay close to each other.
One of them let you choose upgrades if there is any for your submarine and also choose torpedo loadouts and refit your sub.
The other officer is the one you get your missions from.
Talk to him and select the top first dialoge. He will give youa breifing how the war goes on and when he is done you can select what missions you want to do from thos that he offer. Simply find the the little marker on the map where the mission takes place and click the symbol and select request mission.
Now you are assigned a mission. Exit the dialoge. Click on the captain/commander a second time and now choose the other option to start your mission and you will go through a loading sequence and when that is done. You will be on your sub and ready to go.