Peel and slice the eggplant into 1" round slices
Place them on a toweled baking sheet and sprinkle each side with salt - allow to weep for 15 to 20 minutes
While they are weeping, Place the saucepan over medium heat with the olive oil.
Add the onions and saute until they are translucent - about 7 minutes
Raise the heat to high and add the tomatoes and all the other spices
Bring to a boil and reduce heat to low
Simmer for 20 minutes, stirring occasionally
Place the eggplant slices into the zipper bag along with the flour and shake until well coated
Place the dutch oven on high heat and add the oil.
With your thermometer, check until the oil reaches 350 (If you don't have one - place a slice of raw potato into the oil, when it fries and turns toasty brown, your oil is hot enough)
In small batches, remove the slices from the bag and dip them into the egg / water mixture, making sure you coat both sides completely, and transfer to the oil
Cook for about 7 minutes each batch - using your tongs to flip them over occasionally during the process.
When they are golden brown, remove and drain onto paper towels
Preheat the over to 400
In the baking dish, lay the cooked eggplant in a single layer completely covering the bottom
Ladle 1/2 of the tomato mixture over the eggplant
Top the sauce with 1/2 of the Mozzarella and Parmesan
Place a second layer on top of the cheese
Add the rest of the sauce and spread to cover evenly
Add the rest of the cheese
Bake at 400 for 20 to 25 minutes - or until the cheese is brown and bubbly