I doubt the weight of one cheese on top would affect the bottom one too much , unless of course you're making 12 pound cheeses or something big like that.
If you were stacking 4 or 5 high it might also make a difference too.
If you are flipping them in the molds while pressing , I would reverse them every flip though , just to be sure.
Be careful and be sure to work out the weight by factoring in leverage and PSI , I'm a major proponent of light weights , my cheese are all much better than when I first started and was using heavy weights.
I use just enough to get a good knit , it works for me.
Post some pics of your presses when done.