While you can do this ride clockwise or counterclockwise, the goal is to get from Seattle to Victoria and back. You can certainly short cut it by taking your bike directly on the Victoria Clipper, and from there, continue on north along Vancouver Island. Or you can explore Victoria before taking the ferry to Port Angeles and riding back through Port Townsend. One other abbreviated version of this ride can be done by riding up to Sidney from Victoria and taking the ferry back to Anacortes.
All the shortcuts aside, here is the loop I recommend for getting to and from Victoria from Seattle.