Slice the eggplant into 1/2 inch round slices. Arrange the slices on a baking sheet and sprinkle generously with kosher salt on both sides. Set aside for 1 hour to let the bitter juices weep from the eggplant. Meanwhile, make the marinara sauce.
Heat the 2 Tbs olive oil over medium-high heat. Saute the onion for 2 minutes and stir in the garlic. Saute for another minute until lightly browned. Add the can of tomatoes, a sprig of fresh basil and 1/2 Tbs of the dried thyme (or a fresh sprig of thyme if you have it). Bring the sauce to a boil. Lower the heat and simmer for 15 minutes. Turn off the burner, remove the herb sprigs and leave the sauce until you are ready to assemble the casserole.
Heat enough vegetable oil over med-high heat in a large dutch over or high-side skillet to completely cover the slices of eggplant.
Preheat the oven to 400 degrees.
Place the flour in a deep plate.
Whisk the eggs with the milk in another another deep plate.
Combine the bread crumbs, 1 tsp salt, oregano and other 1/2 Tbsp thyme and season well with black pepper in a third deep plate.
Transfer the eggplant to a colander and rinse well with cold water. Blot the slices dry with clean kitchen towels.
Dredge the eggplant in the flour, then dip it in the egg and finally dredge it in the breadcrumb mixture. Shake off any excess breading and lay the eggplant on a baking sheet.
Fry the eggplant in the vegetable oil in small batches. The oil should be 400 degrees. Basically, it needs to be hot. Turn it over once during the frying process and it should be golden brown and crispy on both sides. Remove the eggplant to a baking sheet lined with paper towels. Repeat with remaining eggplant.
Prepare a 13x9 baking dish by brushing lightly with olive oil.
Cover the bottom of the baking dish with 1/3 of the marinara sauce. Arrange half of the eggplant over the sauce. Cover the eggplant with another 1/3 of the sauce. Scatter half of the Parmesan cheese and layer half of the mozzarella over the eggplant. Repeat with the remaining eggplant, sauce, parmesan and mozzarella.
Bake until hot and just beginning to brown, about 30 minutes.