I've never thought about it much, but I have had both a fender and a a rack installed on the back at the same time. Currently the rack is installed in the upper eyelets.

My guess is that it doesn't matter. You just got to make them fit. If the rack fits better on the lower eyelets, put it there. The eyelets are probably far enough from each other that the rack and fender mountings won;t interfere.