The people of the Amazon were semi-nomadic, which made the Inca style of conquest and cultural integration difficult. Furthermore they were known to be violent. This was their best defense against conquest by both the ruling Andean powers and the Spanish/Portuguese. They had little to offer and and everyone else had too much to lose.

There is evidence of economic and cultural trade represented in Andean art. Flora and fauna found only in the rainforest is shown in Andean motifs and goods. Feathers in particular were traded from the forests to the more established civilizations.

Edit: a more direct answer- Yes, the Inca had a pretty good knowledge of the rainforest and the people there. Inca influence came in the form of goods: textiles, ceramics, and food/alcohol. These were in exchange for taxes and allegiance. Because the semi-nomadic people did not deal in goods and currency, nor were they in large enough groups to threaten or aid the Inca, they were relatively left alone.

The Inca Empire and preceding Andean cultures traded with but did not politically control Amazonian peoples. Huertas Castillo writes that Inca people obtained feathers and animal skins from Amazonian peoples such as the Ese Eja and Harakmbut, in exchange for items such as bronze axes (26).