Sauté onion in olive oil about 5 minutes. Add eggplant, salt, and pepper. Cover and cook 10 minutes over medium heat, stirring occasionally, until soft.
Add garlic and bell pepper. Cook 5 minutes more, until pepper is tender. Adjust seasoning.
Remove from heat and stir in almonds and cheese.
For the sauce: sauté onion, chili, and salt 5 minutes until translucent. Add cumin, chili powder, and half the garlic; cook 3 minutes. Add tomatoes and water/juice, reduce heat to low, and simmer 30 minutes, adding remaining garlic and optional cayenne in the last 5 minutes.
Layer tortillas, eggplant mixture, and sauce in a baking dish. Cook 30 minutes, until heated through.