Heres is the best way that I have found to enter Scapa Flow, and I can say it is one of the safer ways of entering this anchorage.

The enterance is located to the West and is inbetween the large island of Mainland and the small island of Graemsay. There is only one ASW trawler that patrols these waters. It is better to sink it if you decide to leave via the same route. Stay close to the coast until you reach the area where the large ships are anchored. From there the best ways out are eathier back the way you came in or to the south inbetween the islands of Flotta and South Ronaldsay. Give it a try for yourselfs and tell me if it is better or worse.