I would say yes....a lot of the tributaries were used like side roads..
I have found several nice points in fields near or right beside smaller creeks.
I believe upland settings, like what you describe, would of had smaller, temporary campsites, but as populations increased, upland settings where used more and more. The truth is, stuff can be found anywhere. I guess I would say, look in the creek, is there good material? Also, is there any landforms that would offer protection? Good luck!
Depends where you are at. In my general area it's common to find paleo sites on the top of hills. A state archaeologist told me that is because of increased surface water drainage / levels from glacier melt. Personally a good spot is a nice high flat spot near a creek. Most of the larger mississippian sites in my area are located on high flat ground. Like most high flat ground, it's usally a distance from a water way. Of course they were growing crops and had pottery by that point and could store water.