Preheat oven to 400. Cook bacon until crispy, set aside to drain. Add squash, zucchini, red onion to already warm skillet and saute in bacon grease for 3-4 minutes, until it's starting to soften.
In a separate bowl, combine 1 cup of cheese and mayo. Remove squash and zucchini and layer half of the mixture into the bottom of the pie shell. Top with half of the sliced tomatoes and then spread cheese on top of mixture, then add half of the chopped bacon and top with seasonings.
Next add remaining zucchini, squash, tomatoes, bacon and top with 1/4 cup of cheese. Bake in preheated oven for 30-35 minutes.