Thanks to all for the replies. I think keeping the families/files separate would be better (and easier), too.
However, I ran into what might be a potential, albeit minor, problem. When I was in the "AncestryDNA Member Match" window, I noticed that I can only link myself to ONE family tree.
So it seems that if I want to see how I'm related to each of my DNA matches, my only option would be to merge all my family files into one. Am I correct on this?