Heat oven to 400 degrees. Wrap garlic in aluminum foil. Cook until cloves are soft, 20 to 30 minutes. Let cool, and squeeze the soft garlic from the cloves; set aside.
Cut 3 eggplant in half lengthwise, and place the 6 halves cut side up on a cutting board. Using a paring knife, cut around the perimeters, leaving a 1/3-inch-wide border and being careful not to cut through skin. Cutting down through flesh, cut lengthwise into 1/4-inch-wide strips. Using a small spoon, scoop out the strips, keeping skin intact. Cut strips into 1/4-inch dice. Set both the diced eggplant and shells aside. Cut the remaining eggplant, skin on, into 1/4-inch dice. Set aside.
In a large skillet set over medium heat, warm 2 tablespoons olive oil. Add onion, and cook, stirring occasionally, until soft and slightly browned, 4 to 6 minutes. Add all diced eggplant, bell pepper, 1/2 teaspoon salt, and 1/4 teaspoon black pepper. Cover; cook, stirring occasionally, until browned, 6 to 8 minutes. If mixture starts to become dry, add the additional tablespoon olive oil. Set aside.
Place couscous in a medium heat-proof bowl. Pour 1 cup boiling water over couscous. Cover with a clean kitchen towel, and let sit until slightly cooled, 10 to 15 minutes. Fluff with a fork. Add lemon zest, ricotta, parsley, remaining 1/2 teaspoon salt, and remaining 1/4 teaspoon pepper. Add the reserved eggplant mixture, the roasted garlic, and cherry tomatoes. Stir to combine.
Fill each reserved eggplant shell with couscous mixture. Cover with aluminum foil. Bake until warm throughout and shell has softened, 20 to 25 minutes. Remove foil, and continue cooking until tops are toasty brown, about 20 minutes. Remove from oven. Sprinkle with parsley, and serve.