Welcome back to the Disney Parks Moms Panel, Marianne!
When needing to transfer from
Disney's Wilderness Lodge to Disney's Contemporary Resort, you will board a "Blue Flag" boat from the Wilderness Lodge boat launch. As far as the order, it will depend on the time of day you are traveling. Typically, the Blue Flag boat travels in a clockwise direction when the launches begin each day at 6:45am, and then reverse direction at some point in the afternoon.
With this is mind, you can expect to travel from Wilderness Lodge directly to the Contemporary the first half of the day, and from Wilderness Lodge to Fort Wilderness and then to the Contemporary the second half of the day.
I hope this helps, Marianne! Please let me know if you have any additional questions. I am here to help you plan a magical vacation.
Faith