Ive been to Scapa Flow three times in the last 4 years, and the previous post is corrrect spend no less than a full week there. These ships are big 600+' long and there is a lot to see. You could spend a week on one of the cruisers to really explore it well.
Where are you traveling from to get there? Maybe I can recommend a travel plan. Weight can be an issue when flying into the Orkneys but there are ferry boats too.
As far as where to stay I highly recommend staying in the town of Stromness which is where most of the dives boats leave from. Some really good restaurants, lively pubs, and plenty of support for your dive group. Go to www.ferryinn.com this inns website has links to some of the dive operators and other Orkney info. Ive been with three operators in the three trips and John Thornton with th MV Karin was the best. Big boat, plenty of room for 12 divers, very professional and a lot of fun.
Figure on 40' vis, depth range from 60' to 165', water temp is 53 degrees, NO current, 2 -3 ' waves. Since all the boats are deep draft you dont even know you are on the water most of the time. Nitrox is available on all of the better boats, they blend right on deck, and you never have to break down your kit until the end of the week. It rains often (2 or 3 times per day) but not for long. It is always windy 20 knots is common, but it had to blow 45 to keep the boats at the dock and that only happened once in 21 diving days I had there. It is mostly cool 50 - 65 degrees in Sept. We were there on the warmest day they had in a number of years and it was 72.
Really is world class wreck diving and they make it very easy on you once you get there.
Nemo