Preheat oven to 400˚F.
Cut eggplants in half, lengthwise. Scoop out the flesh/pulp, leaving a 1/2-inch border around the eggplant shell. Chop up the pulp and set aside.
Place empty eggplant shells on a rimmed baking sheet; season the empty shells with salt and pepper, and let stand cut-side up.
Heat olive oil in a large skillet over medium high heat.
Add diced onions and chopped eggplant-flesh to the skillet; cook for 2 minutes.
Break up the sausage with your fingers and add it to the skillet; stir in garlic and season with parsley, thyme, oregano, salt and pepper, and cook until sausage is evenly browned. About 6 minutes.You can also break up the sausage using a wooden spoon while cooking, but I find it easier to work with it when I break it up beforehand.
Remove skillet from heat and taste the mixture for seasonings; adjust accordingly.
Using paper towels, wipe down the eggplant shells/boats.
Stuff the sausage mixture into the eggplant shells.
Pour hot water inside the baking sheet, around the eggplants.
Bake in the oven for 25 to 30 minutes, or until eggplant is tender.
Remove from oven and sprinkle cheese on top of each eggplant.
Bake for another 5 minutes, or until cheese has melted.
Remove from oven and serve.