Preheat oven to 350°F IN BATCHES, Saute the squashes in a little olive oil, seasoned with salt and pepper, over medium heat until it has broken down and slightly browned, about 15 to 20 minutes, covered at first to release liquid, then stirring occasionally to brown.
Place into large collander in the sink and gently pour the squashes into the collander, allowing to drain 10-15 minutes, Then placing them in a very large bowl. Continue with your next batch until you have cooked all the squashes. (my large skillet took 2 batches).
To the same skillet (now empty), melt the butter and saute the onions, garlic, and bell peppers for about 5 minutes. (season with more salt and pepper if desired).
Remove from heat, and immediately add the crushed red pepper flakes, sour cream, cheddar, and parmesan cheeses. Stirring to incorporate quickly.
To a very large bowl, place all squash, then pour the onion/cheese mixture over top. Stir gently and thoroughly to incorporate the casserole.
Pour mixture into a 9x13 (or larger) buttered casserole dish and top with crushed Ritz crackers. Bake for 30-40 minutes. Let cool 5-10 minutes before serving, allowing casserole to set up.