With the Mass-click feature out now, I think that you can decide
what boxes you want to get clicked, or have none be allowed to be
clicked at all! I know a bunch of people who put Pokemon in their
boxes (myself included) so they don't get clicked. The way this
would work would be with a checkbox a bit bigger than the ones for
the pokemon, and it says, "Block from Mass-Click." You could just
click that and then Mass-Clickers would go right over that box and
move to the other boxes.