Preheat oven to 425°F. Season sliced tomatoes with 1/2 tsp. salt and pepper; set aside.
Heat olive oil in a medium nonstick skillet over medium heat. Add sliced onions and water; cover and cook, stirring occasionally, until very soft, about 10 minutes. Uncover and then season with remaining salt. Cook until the onions are dry, about 5 minutes. Let cool.
Unroll pie dough on one side of a large baking sheet. Spread 3/4 cup cheese evenly on dough, leaving a 1-inch border. Top with half of onion and half of tomato and then sprinkle 1/4 cup cheese on top. Fold border of dough partially over filling. Repeat with remaining piece of dough and other ingredients.
Bake tarts until crusts are golden brown and flaky, about 50 minutes. Let cool for 5 minutes, then cut into large wedges and serve.