There are two basic Ecuadorian tours to the Amazon Rainforest Basin: lodge-based tours and canoe-based tours. In both, you pay a base price at the beginning which includes guides, all meals, transportation from the nearest major town to the launching spot and usually special equipment like boots and rain ponchos. The guides expect tips at the end of your tour. 
Lodge-based tours tend to be a bit pricier and more comfortable. They are best booked out of Quito, where most have their main offices or arrangements with tour agencies. You can expect a variety of quality and comfort: everything from shared bathrooms with cold water to steamy private baths and gourmet meals. The prices for these tours range right around $60-100 per night.
Canoe tours are great for those willing to rough it. You usually travel by day, stopping to spot flora and fauna along the way and enjoy picnic meals. At night you either camp out or stay in a local community where there will be a small hotel. Sometimes homestays are provided on these tours. Canoe tours can be booked in Quito, or for a discount, plan to book in the towns where your tour will begin. Choose from: Puyo, Tena, Coca or Lago Agrio for trips to the nearby reserves. These tours are significantly cheaper than a lodge-based tour.