In a saute pan, over medium heat, add 1 tablespoon of the oil. When the oil is hot, add the onions. Season with salt and pepper. Saute until caramelized, about 4 minutes. Add the garlic. Continue to saute for 30 seconds. Remove from the heat and cool. In a large mixing bowl, combine the yeast, sugar, 2 tablespoons of the oil, warm water, rosemary, and caramelized onions. Whisk until the yeast dissolves. Set aside and let rest for 10 minutes. Stir in the flour, 1 cup at a time, until all is incorporated and the dough has come together. Flour a smooth surface and knead the dough several times. Grease a large bowl with 1 teaspoon of the oil. Add the dough, turn once and cover with plastic wrap. Place in a warm, draft free area and let rise for 2 hours, or until double in size. Preheat the oven to 400 degrees F. Divide the dough in half, working with one half of the dough at a time, divide the dough into 6 pieces. Form each piece into round balls. Roll each ball into 4-inch rounds. Place the rounds on parchment lined baking sheets. Lay 4 slices of the tomatoes over each round of dough. Season with salt and crushed red pepper. Lightly brush the tops of each round of dough with olive oil. Allow the rounds to rest for 20 minutes. Place in the oven and bake for 15 minutes. Repeat the above process with the remaining dough. Remove the pans from the oven and sprinkle each round with both of the cheeses. Place back in the oven and bake until the cheese melts. Remove from the oven and serve warm.