Mounting the rack on the lower eyelet would put the rack a little lower, which is usually a good thing. It may also put the rack a little further toward the rear of the bike, which could also be good if you'll be using panniers. I put mine on the top eyelet just to keep the fender stay from having to cross it, although on my bike the top eyelet is directly over the axle and the bottom eyelet is just hanging off the rear of the dropout. I would think it would be slightly stronger because of this, though it's probably not enough to make any noticeable difference. No reason you can try it both ways and see which you like better!