In a separate bowl, combine 2 cups of the shredded mozzarella with half a cup of the grated Parmesan. This mixture will serve as the cheesy middle layer that melts slowly and luxuriously into the pasta as everything cooks together.
Spoon approximately one third of the sauced mostaccioli into the bottom of the prepared slow cooker and spread it into an even layer. Sprinkle half of the mozzarella and Parmesan mixture evenly over this first layer of pasta.
Add another third of the sauced mostaccioli over the cheese layer and spread it evenly. Sprinkle the remaining mozzarella and Parmesan mixture over this second pasta layer. Finish by adding the last third of the sauced mostaccioli on top, smoothing the surface gently with the back of a large spoon.
In a small bowl, combine the remaining 1 cup of shredded mozzarella with the remaining half cup of grated Parmesan. Sprinkle this final cheese mixture generously and evenly over the very top of the pasta to create a thick cheese blanket that will turn golden and bubbly as the dish finishes cooking.
Place the lid on the slow cooker and cook on LOW for 2 and a half to 3 and a half hours, until the pasta is completely tender but not mushy or falling apart. Resist the urge to lift the lid during the first two hours of cooking — every time you open it you lose heat and add cooking time.
Around the 2 and a half hour mark, quickly lift the lid and test a piece of pasta from the center of the pot for doneness. If it still feels a little firm, replace the lid and continue cooking, checking every 20 to 30 minutes until the mostaccioli is just tender and the cheese on top is fully melted and bubbling at the edges.
