Preheat oven to 425°F. Line two large baking sheets with parchment paper and coat with cooking spray. In a shallow bowl, whisk together almond flour, 1/2 cup Parmesan, Italian seasoning and ½ teaspoon sea salt. Season with salt and pepper.
In another shallow bowl, whisk eggs with 2 Tablespoons water and season with salt and pepper.
Dip an eggplant slice into the egg wash, then sprinkle the almond flour parmesan mixture over each side of the eggplant slice. Place on baking sheet. Repeat to coat all eggplant slices. Spray tops lightly with cooking spray.
Bake until soft inside, and golden and crisp on the outside, about 30 minutes, flipping around the 15 minute mark.
In a large baking dish, add 1 cup of marinara and spread evenly. Add an even layer of baked eggplant slices. Add another 1 cup of sauce. Sprinkle with 1 cup mozzarella, ¼ cup of the remaining Parmesan and 1/4 cup fresh basil. Top with another layer of baked eggplant slices and spread on 1 cup of sauce. Top with 1 cup of mozzarella cheese, ¼ cup parmesan and remaining fresh basil.
Bake, uncovered, until top is bubbly and golden, about 15 to 20 minutes.