500 mile days when we are towing is as much as we ever care to do (usually less than that).
At Bellingham, the charge for one in and out at the ramp is $7.00, I think. Good ramp. Transient docking at Bellingham is very reasonable. You'll have to check with the marina office, but I think there is a 5 day limit for leaving your truck and trailer in the main lot. They do have "long term" parking that is right across the street, and was no charge last time we used it. Bellingham Bay can get a little lumpy, so consider launching and spending the night at their transient dock, then head out fresh, first thing in the morning.
If you have electronic charting, you will see the best routes between the islands... it may look compact on a chart, but there is a lot of water! I'd suggest picking up a Waggoner's Cruising Guide; before your trip would be better, as it would give you plenty to "study" and dream about. There is great info in there for anchoring, marinas, etc, etc.
Tides can run 10 - 12 feet or more, but floating docks are the rule there - easy to tie off. Keep that in mind when anchoring, though. Those tides can create current... remember: wind against current will make for lumpy conditions. Major straits, like Rosario, Haro, and Juan de Fuca, and Boundary Pass will have ship traffic... give them plenty of room and watch for the wake.
Even though you will see depths in excess of 500' in many areas, there are plenty of good, shallow anchorages, if that is your preference.
Friday Harbor has a real grocery store and a variety of restaurants; it is the commercial hub of the islands, but it still a small town. The staff at the Marina (Port of Friday Harbor) are professional and friendly. A night on the dock there allows you to resupply, take showers, etc.
Roche Harbor has some big dollar boats that don't see a lot of use, but they also have plenty of space for boats our size. A small grocery store, and interesting walks nearby.
I forgot about Jones Island (mentioned by DogDuckTitus) - the entire island is a state park, and the only way to get there is by boat (or kayak - a lot of the kayak excursion companies use Jones Island because they have potties).
While I am partial to the wide variety of wildlife, the San Juans are breath-takingly beautiful. You can make a week there as rustic or as posh as you like... or a fun combination of both.
At first blush, cruising in the San Juans can seem intimidating for those not familiar with the area - all those islands! You will more likely find it to be a wonderland as a boater. Watch the weather, know where you are at all times, then decide where you want to go. Don't try to do it all in 5 or 6 days... the things I posted will give you some highlights. For perspective, it is just over 27 miles from Bellingham to Friday Harbor.
This is just personal preference, but a fun way to spend 6 days would be:
Day 1 - Bellingham
Day 2 - Bellingham to Sucia Island
Day 3 - Sucia Island to Friday Harbor
Day 4 - Friday Harbor to Reid Island
Day 5 - Reid Harbor out to the west side of San Juan Island to look for whales, then into Roche Harbor
Day 6 - Roche Harbor back to Bellingham (34 miles)
Celebrate your return to Bellingham with a nice meal at Anthony's, right at the marina.
You will feel like an island-cruising salt-water pro, and will have seen some beautiful places... then start scheming on how you will take more time on your next trip to the San Juans.
Have fun with it, keep us posted.
Best wishes,
Jim