I would play it by ear. Look at La Conner as a decent stop over. I would think that it would be nice to get further than Annacortes. Beyond La Conner on the East side of Whitney Island opposite the southern tip of Camano Island is Langley. It is a small place but very friendly and there are a couple good places to eat up the hill in the town of Langley.
Further South is Everett. Big place and they should have lots of transient slips available. Not a lot there from my memory, it is a big place.
Even further South you could stop in at Kingston in Appletree Cove. It is west a cross the sound from Edmonds. It is a great stopover spot and it would be a relatively short run to Elliot Bay the next day.