I went to Orkney seven years ago though only briefly - spent the night (which never really got dark) on an overnight ferry to Shetland. Stromness was the first place I saw and liked it a lot - only there for a couple of hours but found a great bookshop where I bought the The Collected Poems of George Mackay Brown. The group I was with did spend some time in Kirkwall later on and I was quite impressed by St Magnus Cathedral - beautiful stained glass windows. It was from Stromness we traveled to Skara Brae, the Ring Brodgar and Stenness - so it may be a good place to base yourself. Sorry I can't help with specific B&Bs but am sure someone here will be able to.