Slice the yellow squash into 1/2-inch thick rounds and thinly slice the yellow onion into half-moons. In a microwave-safe bowl, combine the squash and onion slices. Add the water, kosher salt, black pepper, garlic powder, Italian seasoning, and crushed red pepper flakes. Toss everything together so the seasonings are evenly distributed throughout the vegetables. I like to season before microwaving rather than after—it allows the flavors to infuse into the squash as it cooks rather than just sitting on the surface.