[Corsair]

You have to get to either a support submarine (milkcow) or a resupply cargo. Places and availability dates are in the F1 screen. Once you are near one of them you Esc and Dock at... If you are using SH3 Cdr 2.7 it will know it's a refuel stop and only take off one day. After this you start a new patrol with a null grid : means you go back to home base and free to hunt on the way. Through SH3 Cdr you can also manually assign a new patrol grid.
If you don't use SH3 Cdr there is a utility called SH3 Patrol 1.6 that does the same job.
All this is assuming you are playing with one of the supermods featuring the refuel/rearming boats.
If you are playing with GWX 1.02 you can now also dock at any friendly base without bug. (but not sure if you can refuel/rearm there...)

PS : Welcome to Subsim !!