Salt the eggplant slices and arrange on a cutting board. Press a plate or board on top and weigh down with a heavy object.
Let rest to remove water from the eggplant while you prepare the sauce.
To a large saucepan, add olive oil, garlic and onion. Cook until onion is translucent. Add tomatoes, thyme, salt and pepper.
Bring to a boil, then turn to medium-low. Cook with lid partially on, about 40 minutes.
Add milk, flour and butter to a sauce pan.
Bring to a boil, then lower heat, stirring constantly until mixture thickens.
Coat the bottom of a baking dish with tomato sauce. Layer eggplant slices, more sauce, sprinkle of Parmesan, mozzarella and bechamel. Repeat until all ingredients are used.
Bake at 350°F for about 45 minutes. or until bubbly.