Quick answer.. unfortunately you can't explore the Amazon on your own; you will always need a guide to take you anywhere. The choice you need to make is more between staying in an eco;lodge or a pousada. The former are mainly way off the beaten track and the price (expensive) includes full board, transfers and guided tours. Alternatively stay in a pousada and contract day trips out with local guides. This way you have much more freedom and it costs you less, but you don't get that all enveloping jungle experience.
You can find information on both jungle lodges and pousadas on www.hiddenpousadasbrazil.com.
Cheers, Alison almost 8 years ago