The Amazon bassin spreads over 6 Ecuadorian provinces : Sucumbíos, Orellana, Napo, Pastaza, Morona Santiago and Zamora Chinchipe.
Ecuadorian amazon is mainly tropical rainforest elevated 400 m above sea level.
The Amazon region of Ecuador is one of the few places in the world where its probably best to travel with a group, with a guide or through a jungle lodge. Unless you are studying, teaching English or consulting on a project in the Amazon, you are unlikely to have enough knowledge about the area to stay safe and, most importantly, to learn about the plants and animals that make the area so special.
If you have more than a few days and you're not a super tight budget, staying and traveling with a jungle lodge can be very rewarding. You're based right in the midst of the jungle, and, at the better lodges, you're in an area that's protected from farming, logging and drilling. You usually have 2-3 activities per day including birding hikes, canoe trips and fishing for piranhas. Again, at some of the better lodges, you usually have a guide that speaks English, French, etc and an indigenous guide. This ensures that you really get to see some amazing things like five different species of monkeys, caimans, tarantulas and lots and lots of birds.
For hard-core birders, most of the lodges offer special sight-seeing activities with much earlier wake-up calls.
Typically, you pay one daily fee that includes transportation to/from the airport, accommodations, meals and guides, and then snacks, alcohol and tips are over and above the fee.
Fees range from under $100USD to well over $250USD/night depending on how you booked your stay. If you book directly with a lodge or if you book through an Ecuadorean travel agency, you generally get a better deal than one in your home country.
Visiting indigenous communities is usually really expensive and very hard to reach. They are usually really deep in the jungle and access to them is only available by small Cessna planes. There are also some luxury lodges which were foreign investments but now are owned by the community.
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.
You can Find a lot of possible actives
You can travel alone or get some of the tours that the tourist agencies offer for this region of Ecuador.