I went to Orkney a few years back, flying into Inverness and hiring a car (picked up from airport) Drove up to Gill's Bay and caught the ferry over to the island staying at Finstown which was a good if not quite place. The car came in very handy and is a must for touring the various Mainland and South Ronaldsay sites especially if time is short.
I also visited Rousay and Eday taking the car with me. However it would have been nicer and easier (and cheaper I would imagine) to take a pushy. There are many sites to visit on these islands but all are easily to get to on a bike. Beware ferry times and days, if i remember it was a bit of a task organising myself to get to the islands in to the week I was there (on top of everywhere else i visited) as not all ferries operate all week. Kirkwall has plenty to see and do including the museum and St Magnus Church but if I did it again I would stay in Stromness. I continued with my journey in the car and drove to Ullapool and over to the Western Isles to visit Callanish and plenty of other places along the way. Hope to do it again one day it was a fantastic experience.