Can you give us an idea of exactly how many nights you plan to spend in Europe? That helps to define how many days you have to explore. The typical way to count is that to have a full day somewhere, you have to spend 2 nights there. So 4 nights gives you 3 days and 5 gives you 4.
With 5 of you, renting an apartment may be your best housing solution. I've rented apartments with my husband and by myself in many countries including The Netherlands. My favorite source to locate them is Booking.com. Keep in mind that a listing might say it's a 2 bedroom, but is counting a sofa sleeper in the living room as a bedroom. The genders of your kids may affect how many bedrooms you actually need.
If you decide to search for hotel rooms as well, it is highly unlikely that you will find one room for all 5 of you. When you do your initial search on Booking.com, you will put in 2 adults and 3 kids. You will then be required to put in the ages of the kids. That's to help determine the bed sizes required. The 14 year old will definitely be counted as an adult. If the 11 year olds are not 12 at the time of your trip, they may not be considered adults, but they'll still need normal beds of some kind.
I've frequently flown from Seattle roundtrip to Amsterdam nonstop both ways and that's worked well for me. I hope you mean nonstop when you say direct. I love flying from the Pacific Northwest because it's a relatively short nonstop flight. However, if the kids haven't done an overnight flight before and possibly for the adults too, jetlag may be an issue.
I totally agree with the person who encouraged you to have the kids get involved in the planning. Many years ago our son took his 2 oldest daughters to Paris. The 10 year old took an active part in the planning. The 12 year old didn't. Can you guess which one had the most fun?
There are some good resources right here on the Rick Steves website that the whole family would benefit from exploring.
Travel Tips has the basics of European travel in the major categories. If you haven't looked there, the information is great for learning about things you didn't know you needed to know: https://www.ricksteves.com/travel-tips
Explore Europe has specific information on countries and the cities within them. This link is to The Netherlands, but from it you can get to other locations: https://www.ricksteves.com/europe/netherlands
For all things train related there's the Man in Seat 61. This link is to information for trains to and from Amsterdam, but there's much more you may want to learn there: https://www.seat61.com/international-trains/trains-from-Amsterdam.htm
I'm sure you'll get lots of recommendations for places the family could enjoy together. I'm going to suggest the Dutch Open Air Museum in Arnhem: https://www.openluchtmuseum.nl/?taal=en This is a place I've never been that I would absolutely love to visit.
It's not a long train ride, but there's enough to do and see in the Arnhem area that spending 3 nights wouldn't be overdoing it. And in October, the De Hoge Veluwe National Park nearby should be lovely: https://www.hogeveluwe.nl/nl/ontdek-het-park
I must admit that Arnhem is kind of a special place for me. I had my first taste of Nutella at a hostel I stayed at there on my first trip to Europe in 1977-78. I went there specifically to go to the Kröller-Müller Museum: https://krollermuller.nl/ It's in De Hoge Veluwe National Park. I did it all by public transportation, which is much better now than it was 47 years ago.
Finally, at least for now, I'm assuming that you're planning this trip for this year, October 2024. It's obvious, but our son almost screwed this up for his 2nd trip with daughter #2 -- make sure everyone’s passport is current by whatever rules apply for Canadian citizens.