I also used CNH. Try to schedule a week when Juan Salcedo is the guide. He will keep the kids busy. I was already in Ecuador, so you can pick up the trip morning they fly to G Islands. You can then do the Amazon portion on your own, before or after GI. I would recommend the Napo River area, not the region further south that is in theory Amazon-like but is impacted by the amount of oil and mining produced in the area. These are the cheap backpacker lodges that you can get to by bus to save additional airfare.
I liked Sani Lodge as a mid priced experience. They have tenting options to save a few more dollars. Booking diverts you to an agent in Quito and they can help you book the flight. You fly to Coca where the lodge boats pick you up and take you up the Rio Napo. Then there is a short walk on raised boardwalks to where you get into canoes the last leg of the journey. It is an easy adventure. Stays are usually 3-5 days. 3 or 4 are ample unless you are a birdwatchers or have a specialty.
It is the jungle so most places don't allow you to wander around, you will be part of a larger group unless you pay more for a private guide...which might be of consideration for your family