Pre-heat oven 400 degrees F.
Lay the eggplant in one layer on three sheet pans and brush each side with olive oil. Season with salt and pepper. Bake for 15 minutes. Remove trays from oven. Turn the slices over and rotate the trays 180 degrees and place back in the oven and bake for another 10 minutes or until tender.
In a 10 x 14 x 2-inch baking dish, spoon one cup of the sauce and spread evenly on the bottom. Place a third of the eggplant on top in one layer. Scatter a third of the basil, a third of all the cheeses on top. Repeat twice, starting with the marinara sauce and ending with the parmesan, making sure each layer is evenly distributed.
Place cubed bread in a bowl.
Over low heat, melt the butter in a small saucepan with fresh thyme and garlic, and let it cook for a few minutes. Fish out the thyme and discard. Pour the melted butter mixture over the bread cubes and toss evenly to coat. Season with salt and pepper to taste.
Spread the seasoned bread mixture evenly over the eggplant. Place on a baking tray and bake for 20 – 30 minutes. Let rest 10 minutes to help cheese settle before serving.
To serve, add 1/2 cup warmed marinara sauce to a plate, top with slice eggplant Parmesan and drizzle the pesto around the sides.