This simply covers the connection between Sidney and Seattle. First, catch the ferry from Sidney, then you have the following choices:
1) You can ride to Mt Vernon Amtrak and catch the train to Seattle or Vancouver
2) You can ride north to Bellingham and catch Amtrak from there. This is a more attractive option than the above.
3) You can ride south from Anacortes down Whidbey island to return to Seattle. I would recommend spending the night in Port Townsend or Coupeville before completing the trip to Mulkiteo.
Below is the map for option 1: