Do it on your on. You have enough time to see them both in one day. I recommend you to buy tickets by internet, is cheaper and very easy.
Do it on your own. Look at the time tables in Boeing the future of flight and in the museum of flight. Choose your starting point. City centre is in between
Take a guided tour.... everett is the boeing tour and is colocated with the future of flight museum. InnRenton there is another flight museum (https://www.museumofflight.org/) and on the outskirts of Portland there is the evergreen museum (https://www.evergreenmuseum.org/) all are worth a visit... Everett and Renton are the two boeing factories.
the factory only gives guided tours and they are 90 min long. we did not do museum but you can do both in one day. you do need to purchase tour tix in advance.
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