Early in the war I will try to complete 3 or 4 missions, by than fuel and arms are low so I just don't call in and RTB when I have to. Completing missions will get you a better boat sooner. I also have a 60 day more or less, limit on any patrol, refits or not. Out of Pearl I fuel at Midway on the way out and if necessary on the way back.
The only time I refit is when something unusual happens very early in a patrol. EX just pulled out of Midway on my way to Japan and ULTRA advised about the IJN invasion task force. Intersected the TF and used most of my torpedoes. I did a refit at Midway and than continued to Japan. Had huge tonnage on that one as I sank 3 CV's in the TF and found a very good convoy near Japan. Feeling real good about myself and when returning to Pearl I hit one of those small islands near Midway and almost sank my boat.
If you keep calling in they will keep giving you new missions, very seldom get a RTB order so 60 days seems the best. If you don't complete a mission it's no big deal if you've sunk enough ships.
At least in this game Fleetboat captains have a lot of discreation.
Magic