I thin the smaller fruit whether on the top or bottom. If it looks like a branch will touch the ground at harvest (with the weight of the fruit - in other words lower branches) then I remove the ones on the bottom so they don't touch the ground when the branch does.

For branches higher in the canopy, I remove the fruits on top of the branches more often because I've noticed a little more bird damage on fruits on top of the branch. I think it's more convenient for birds to perch on a branch and peck at a fruit on top of the branch. They don't have to bend down much.

Personally I don't know that it matters all that much if you thin on top or bottom, but I do know that a lot of folks will purposely thin all the fruit towards the bottoms of branches because they tend to be more shaded by leaves on the same branch and thus might not color up as well as fruits on the sides or top of the branches.