Three threads come up in this forum when you search for San Juan; there's some good info in them.
The Washington State Ferries website has lots of info. For example, for the Anacortes terminal, there is info on parking, shuttles from SeaTac/Seattle, bicycle loading procedure, etc.
There are inter-island fares, but a round-trip ticket to Sydney allows multiple on/offs on the eastbound leg (if I'm reading their fares table correctly):
Googling for "San Juan Island parks" turned up some info, including http://www.sanjuanco.com/parks/