Using three pizza stones of the same size works. But they really do need to be of the same size. One goes into the oven. The other two are used to set up the transfer.
The general methodology is as follows. It is assumed that the fresh dough is prepared but has not been removed from its work surface. It is also assumed that the first pizza stone is already in the oven.
STEP 1: On a separate work surface place the second pizza stone. Apply a thin film of grapeseed oil to the stone and then dust it very well (and very uniformly) with cornmeal or grits. Carefully lay the fresh dough across it, being sure not to slide it around. (Folding good, sliding bad.) Now, assuming there's an overlap, here's a great opportunity to easily complete two common tasks. First, go round and gently push in a bit of the dough so that the border becomes just a bit puffier than the rest of the pizza. The height and firmness of the stone makes it easy to get this just right. (You can even fill a fold with thin strips of fontina or fresh basil.) Second, use your pizza wheel to trim off all the excess dough. The stone makes the perfect border for that task, especially if placed on a turntable.
STEP 2: Add your fresh toppings (as soon as possible). Sprinkle a trail of cornmeal all round the very top edge of the crust. Then place the third pizza stone on top. Either side is fine. Just line it up. Now grab the whole thing with both hands and flip it over. Set it on a round cutting board, like the ones used for cheese, the diameter of which is less than that of the pizza stone. Room enough for your hands is the idea. Now remove the first pizza stone, thus exposing the pizza's underbelly.
STEP 3: Open the oven, pull out the rack, and leave it that way. This won't take long. Using two pot holders, remove the heated pizza stone from the rack and flip it over so that the cooking surface is facing downward. Place it squarely onto the bottom side of the pizza which, of course, is the side now facing up. Now immediately grab the whole thing with both hands, flip it all back over again, and place it onto the center of the oven rack. All that's left is to remove the cool pizza stone from the top of the pizza and close things back up.
Of course it may seem excessive to own three pizza stones. But there are other considerations. Take this same process for example and apply it to making a pair of calzones. For STEP 1 you would have to avoid puffing or trimming the crust, at least at first. And in STEP 2 you would be placing another layer of dough on top and then stuffing/folding/primping/trimming to your own personal specs. However, in the part of STEP 2 where normally you would utilize a cool second pizza stone, instead you will be using a second heated one. Just be sure first to lightly dust the top of the dough with cornmeal too.
This time there's no need to flip the thing before placing it onto the oven rack. You just put it there and leave it that way. In other words, the second heated stone stays right there on top of the calzones, at least for awhile. Then, not long before midway through the baking process, you open the oven door, pull out the rack, flip over the whole thing, and remove the topmost pizza stone before closing things back up. (So you're removing the stone that was on the bottom.) In this way you have ensured of evenly cooked calzones with a nice crust on both sides.
You will possess therefore only one extra pizza stone, not two. And even here, there's something to be said for having a cool one out and ready when the calzones are done. Transferring them to a cool stone stops the cooking process (prevents overcooking) and, obviously, promptly promotes the cooling process while at the same time providing a good cutting surface. Plus, honestly, you don't want to gunk up a pizza stone. It's good for that spare to be used just for slicing and serving, as it still possesses that touch of authenticity. The other two should never see aught but dough, and should be stored facing each other.