Heat the olive oil in a large pot over medium heat. Add the onions and cook until soft and translucent, 10 to 15 minutes. Add the tomatoes and reduce the heat to low. Cook, stirring occasionally, for about 2 ½ hours.
Remove from the heat and, using an immersion blender, blend until smooth, adding basil leaves as you blend.
Lay the eggplant slices in a single layer on a cooling rack set over baking sheets; season with salt. Let stand 15 minutes to release moisture; then pat dry.
Place the flour in a shallow dish, and dredge the slices through the flour.
In large pot, heat the canola oil to until a deep-fry thermometer reads 300 degrees F.
Add the eggplant slices to the hot oil and cook, turning once, until lightly browned. Drain the fried eggplant. Place both cheeses in the food processor and combine. Add the basil leaves and olive oil. Season with fine sea salt and pepper.
Preheat the oven to 350 degrees F. Set ring molds in a large shallow baking dish.
Place a dollop of tomato sauce at the bottom of each ring mold. Top with a slice of eggplant. Add a layer of cheese to each mold. Top with another dollop of sauce, followed by another slice of eggplant. Repeat the process until you reach the top of the ring mold or create four layers, ending with a slice of eggplant. Top with a little tomato sauce. Transfer to the oven and bake until the cheese melts and eggplant is warmed through, about 15 minutes. Carefully remove the ring mold and serve.