Step 1

Put a pizza stone on the lowest rack of the oven, heat the oven to 550°F, and let the stone heat for at least a half-hour.

Step 2

In a 12-inch skillet, heat 1 Tbs. of the olive oil over medium heat. Add the onion and a generous pinch of salt; cook, stirring occasionally, until soft and well browned, 15 to 18 minutes. Remove from the heat and let cool.

Step 3

In a large bowl, combine the remaining 2 Tbs. olive oil with the garlic, chives, thyme, and a good pinch of salt. Add the zucchini and squash and toss to coat. In a small bowl, combine the two cheeses.

Step 4

Lightly flour a pizza peel. Stretch one dough ball into a 10- to 11-inch round and transfer it to the peel. Top with half of the caramelized onion and just enough cheese to cover the onion. Top with half of the zucchini and squash, alternating colors and direction and slightly overlapping them; the squash does not have to cover the whole pizza. Sprinkle with a little more (about 1/2 cup) of the cheese.

Step 5

Slide the pizza onto the hot stone and bake until the cheese is melted and the crust is nicely browned, about 8 minutes. Transfer to a cutting board and sprinkle with sea salt and crushed red pepper flakes, if using. Repeat to make the second pizza.