This depends mostly on how much money you have to spend. If you're staying at one of the jungle lodges, you'll be picked up at the airport either Quito or Coca. Depending on how deep you're going, your boat ride will be anywhere from 3-6 hours long...or more.
If you're not staying at a jungle lodge, you can usually hitch a ride on one of the boats plying the rivers. Just be sure to bring a rain poncho to protect against frequent afternoon storms. If boating's not your thing, there is a system of buses to get into the interior, but the trips are very long.
