We tow to Anacortes, WA and launch and retrieve the boat using their very reasonably priced lift at Cap Sante Marina. I have always used lifts and have never put our trailer in the water. I store the boat trailer for the Summer in a secure storage facility called On Deck Marine. Cap Sante marina allows long-term, free parking of your truck in their parking lot.
Now to the specifics of your question, we don't have a Summer slip for the boat. There are numerous marinas in the San Juan and Gulf Islands that you can get temporary guest moorage in. We usually go further North into Desolation Sound and the Broughtons, where there are also many marinas. But we prefer to anchor out and go to a marina every 4 or 5 days. You have to plan ahead for a marina around 4th of July and Labor Day weekends, but otherwise there has never been a problem getting a temporary slip. Our first year we booked a three month temp slip near Victoria Canada to use as a base of operations. It was a waste of money as we were seldom there because there are so many beautiful, new areas to explore. Use the Waggoner Guide and the book Best Anchorages of the Inside Passage for info on anchorages and marinas. You will also want to have Ports and Passages available to time your passage through some of the narrow spots. These passages are non-events if you transit them at slack tide.
The PNW is the best boating area we have experienced. We have done this for 4 Summers and have only scratched the surface of all the places to see and anchor. You will love the experience.