I've done it a couple of times, and stayed at a mixture of campsites, hostels, pubs and B&Bs. Some of my favourites were:
1. the Sportsman; a cracking pub up near the top of Dentdale
2. George Inn, Hubberholme; ditto, in Langstrothdale (upper Wharfedale)
3. Kettlewell YHA: nice little village, nice friendly hostel
4. New Inn, Appletreewick: fine country pub
There's not a lot of accommodation between upper Wharfedale and Dentdale, and between Sedbergh and Windermere, so don't leave it to chance.