it's not all that deep there....
Seriously though, I've only done Scapa twice, once in a type II mind you, but if you're running out of air you're going to have to do something drastic because once you fire off them eels you're not going to have time for a breather, what with shore-batteries, patrolling DDs and other fun stuff.
you neglected to mention what boat you're driving so I'm going to assume a type VII for the moment.
Since this is early war and they're definitely not expecting you my thought is that surfacing while as far away from that DD as you can get and going to decks awash, say set depth for 7 meters and being very very quiet, and at a dead stop for half an hour will refresh the air in your boat. The batteries are a different problem but you shouldn't have used up too much juice.
This also gives you a good opportunity to observe the DDs patrol pattern and plan your attack course and where an when to shoot which torpedo, or even calculate a spread pattern that will take out everything you want to hit in one volley.
If you don't get noticed, very quietly go to PD again and commence your attack...
If you do get noticed...well, you were doomed anyway so that's allright
another suggestion if I may, called it an intelligence report if you will,...why not loiter for a few days about 50km west of where you are now, who knows what might come steaming your way...