Preheat oven to 450°F (230°C). Place 1 tablespoon of oil on each of 2 jelly roll pans. Use an offset spatula or your hands to entirely coat each of the pans.
Divide the eggplant slices between the 2 pans, leaving a little space between the slices. Bake the eggplant for 25 minutes. After 15 minutes, switch the pans on the racks, to ensure even browning.
To make the sauce, place the remaining 2 tablespoons of oil into a medium saucepan and heat it over medium heat. Add the onions and cook for 5 minutes, stirring occasionally. If the onion starts to color, turn down the heat. Add the garlic and cook for 5 minutes, stirring occasionally. Add the oregano, basil, pepper, sugar, red pepper flakes, and salt, and stir. Add the crushed tomatoes and bring the mixture to a boil over medium-high heat. Reduce the heat to low. Cover the pan and simmer the sauce for 25 minutes.
After 25 minutes of roasting, turn over the eggplant strips and roast them for another 5 to 10 minutes, until they are fork-tender and browned. Cook the pasta al dente, according to the directions on the package, and then drain it; do not overcook the pasta.
Preheat the oven to 400°F (200°C). Place the pasta in a 9 x 13-inch (23 x 33-cm) baking dish. Add the baked eggplant slices and sauce and mix well.
Cover the pan with foil and bake the eggplant for 40 minutes. Uncover the pan and sprinkle the cheese on top. Bake uncovered for another 5 minutes.