Place the tomatoes in a colander in the sink in 1 layer. Sprinkle with salt and allow to drain for 10 minutes.
Use a paper towel to pat-dry the tomatoes and make sure most of the excess juice is out. (You don't want very wet tomatoes or your pie will turn out soggy).
Heat a large skillet over medium-high heat. Season zucchini and squash with salt and pepper. Saute the squash in a single layer for 2-3 minutes on each side or until golden brown. Remove to a paper towel
Layer the zucchini, squash, tomato slices, and onion on the bottom of the pie shell. (Make sure pie shell is pre-baked, and completely cool, to avoid sogginess). Sprinkle basil on top.
Combine the grated cheeses and mayonnaise together. Smooth cheese mixture over the top and sprinkle parmesan cheese on top.
Bake for about 30 minutes or until lightly browned. Allow to cool for at least 15 minutes.
To serve, cut into slices and serve warm.
Make Ahead Instructions: The squash, zucchini, and onion may be sliced up to one day ahead of time. The cheese spread may also be made ahead and just kept in the fridge.To Freeze: I don't recommend freezing this recipe because the vegetables may make the crust soggy when it thaws, and the mayo in the topping doesn't freeze well. You may use a frozen, thawed pre-baked pie shell, to save time.