Prepare the Ratatouille: Heat olive oil in a large skillet or Dutch oven over medium heat. Add the diced onion and sauté for 4-5 minutes until softened. Add the garlic and cook for another 1 minute until fragrant.
Cook the Vegetables: Add the zucchini, eggplant, red bell pepper, and yellow bell pepper to the skillet. Cook for 5-7 minutes, stirring occasionally, until the vegetables start to soften. Stir in the tomato paste and cook for 1 minute. Add the diced tomatoes, thyme, oregano, red pepper flakes (if using), salt, and black pepper. Reduce heat to low, cover, and simmer for 20-25 minutes, stirring occasionally, until the vegetables are tender and the flavors meld. Stir in the fresh parsley and basil just before serving.
Cook the Orzo and Quinoa: While the ratatouille simmers, bring the vegetable broth (or water) to a boil in a medium saucepan. Add the orzo and quinoa, reduce heat to a simmer, and cook for 10-12 minutes, or until both are tender and the liquid is absorbed. Fluff with a fork, then stir in the olive oil, fresh parsley, basil, and a pinch of salt.
Serve: Divide the herbed orzo and quinoa among plates, then top with a generous portion of ratatouille. Garnish with extra parsley and basil leaves. Serve warm.