Hi!
We went to the jungle in Parque Madidi last week. My brother was in Manu, and it was really worth he said. Madidi is much cheaper, and we really enjoyed it. If you want to visit Madidi, you have to go to Rurrenabaque, a town on the river Beni. From there on, you can also do tours to the Pampa, where you can see lots of animals (it's hard not to see them), but thats more touristic. In the jungle there are less animals, but it's nicer to see them because it's hard...
We did both tours with Fluvial tours, for 500 Bs. each. We did not really enjoy the "eco-tourism" approach of our guide of the Pampa tour (Fernando, El Mejicano). For example: he pulled an anaconda out of his hole in the tree, only to show it to us... I did not really like this... Our guide in the jungle was really good: he really was in love with nature, Juan Carlos is his name!
Conclusion: want to see animals (crocodiles, turtles, even some pink river dolphin, if you're lucky an anaconda): go to the pampa, but close your eyes for tourism (there is even a bar on the river bank), want to enjoy nature and hear (and sometimes see) animals: go to the jungle
greets,
Samuel