I added the Mapuche (south Argentina and Chile) the Amazonians (Brazil, some Peru, Colombia, Ecuador and Venezuela) and Chaco (Bolivia) as indigenous groups. Mapuche will be their own bonus, same with Chaco, the Amazonians will have their bonus in Brazil but will need the lands in the rest of the nations to get the superbonus, I already uploaded the map showing how they would look (Chaco is already mapped and some Amazonians too since I already did Colombia, Venezuela, Ecuador and Peru, if what Im doing isnt what you expected let me know so I can hear suggestions
Local indigenous tribal groups, they were not remotely unified in any way that resembles a nation, and often fought amongst themselves. It's like claiming the berbers had full control of the entire Sahara. While the government of Brazil did not apply pressure on the region (not sure about other governments), whenever there was something of interest in the general vicinity of those tribes, they'd get pushed around. Brazil had de facto control of those regions, undoubtly. Also, pretty much the entire of the Amazon river's basin was patrolled semi-frequently by the government.
Alright, I will give Bolivia the cores instead of Brazil, but it'll be controlled by Amazonians
It belonged to Peru until the dissolution of Peru-Bolívia, when it passed on to Bolívia. From there on it was controlled by them, but with little policing due to lack of resources or accessibility. By 1840, it should be owned and controlled by Bolivia, at most with Peru laying some very dubious claims to it.
If I may suggest, Acre should be part of Bolivia, the Amazon river basin should be made into a string of territories, and the inner amazon should really be empty space, with the background colored after the same color of the country superbonuses, being completely impassable by troops.
Here's an image of the basin and it's bigger subsidiaries:
https://upload.wikimedia.org/wikipedia/commons/thumb/0/0d/Amazon_river_basin.png/220px-Amazon_river_basin.pngHelpful reference by EmperorTigerstar:
https://youtu.be/UULp33MNNNE?t=2m56sImperial Provinces of Brazil in 1822 (remained the same in 1840, aside from the Ragamuffin rebellion)
https://upload.wikimedia.org/wikipedia/commons/thumb/6/65/Brazil_%281822%29.svg/1024px-Brazil_%281822%29.svg.pngMore on the Riograndense Republic (rebelled in 1835, ended in 1845, should control the state of Rio Grande but largely identified as rebels and claimed by Brazil):
https://en.wikipedia.org/wiki/Ragamuffin_War