A supervisor at my work asks this question all the time.
He says there are books and books on the American Indian about all their habits, etc, plus movies, stories, and other sources of info on them, but he says nothing ever mentions were they dropped a deuce.
Archeologist have dug 1000's of old sites, digging up all kinds of artifacts, but he has never heard of them hitting any petrified turds.
Pooping technology really has played a pretty significant roll in history. I was watching something the other night about the battle of Alamein in WWII really came down to pooping technology. Germans just pooped in holes. British made little commodes and protected the poop from attracting flies. The Germans had much higher rates of sick soldiers and were generally much less healthy because of it.
I actually watched something on Discovery on whatever tribe of Indians lived up in the mountains in the American Southwest (Hopi?). On this special, an archaeologist found a cave that was full of fossilized poop from Indians. The archaeologist actually said that cave must have been the bathroom for the Indians that lived around that cave. Can't believe I remember that and that I ever actually had the occasion arise in which to talk about it.