here's the state ferry schedule http://www.wsdot.com/ferries/schedul...x?route=ana-sj
There's also information about the terminals - Anacortes has a pay parking lot that allows long term parking near the ferry terminal.

I've not actually been to the San Juans... I keep meaning to try to get up there, but the ferry schedule makes it a bit of a logistical difficulty to make it a day trip....