Brazil actually merged the freed slaves into society because people at the time thought that over several generations, everybody would end up being white again. In a different way they were also trying to suppress them.

As for the indigenous population, before Portugal arrived here there was one large tribe already dominating all the others. The Portuguese then negotiated with that large tribe and that one tribe's culture managed to survive, but the colonizers also had no respect for it or any of the others and grouped them all together as if being the same thing. The other cultures ended up being either absorbed or erased by that larger tribe.