Ditto the others. We chartered out of Anacortes a couple of July's ago - and while we made slip reservations for Roche and Friday Harbors ahead of time, I'm not sure we needed them. There was also ample room on mooring balls in all the popular spots.
We picked up Migael Scherer's "Cruising Guide to Puget Sound and the San Juan Islands" and "Exploring the San Juan and Gulf Islands" Cruising Guide by Don and Reanne Douglass ahead of time. We had never cruised in the area - and these books were invaluable in helping us plan. For our first trip, we stayed in the San Juan Islands the whole week, but won't hesitate to venture further next time.
We didn't find the lack of shoreline access to be an issue, with so much water to explore, getting out wasn't a priority. We did spend a nice afternoon wandering on Stuart Island while moored in Reid Harbor.
I would add that at least one night in Roche is mandatory. No matter what your perspective, the evening flag ceremony and the mega-yacht bunch are worth the fare for one evening, not to mention a decent meal and shower.