Cut 5 crosswise slices from center area of each eggplant, about 1/2-inch thick, to total 10 slices. Peel and dice remaining pieces of eggplant.
Heat 2 tablespoons olive oil in a large skillet over medium-high heat until oil is very hot. Sprinkle eggplant slices lightly with a pinch of salt and cook in hot skillet in batches until slightly softened, about 3 minutes per side. Set eggplant slices aside on paper towels.
Heat 1 tablespoon olive oil in skillet and cook garlic for about 10 seconds; add diced eggplant and season with a pinch of salt and red pepper flakes. Saute until eggplant is softened, about 5 minutes. Pour in marinara sauce and water. Turn heat to medium-low and cook until eggplant is tender, about 15 minutes; stir occasionally. If sauce gets too thick, add a little more water.
Combine ricotta cheese, 1/2 cup Parmesan cheese, pepperjack cheese, a pinch of salt, and a pinch black pepper in a bowl until thoroughly combined. Spread about 2 tablespoons cheese mixture over each eggplant slice. Fold eggplant slices in half to enclose the cheese mixture.
Spread about half the sauce into an 8x8-inch baking dish. Lay folded eggplant slices in a single layer into the dish. Spread remaining sauce over eggplant slices.
Combine bread crumbs, 1/2 cup Parmesan cheese, and 2 tablespoons olive oil in a bowl; mix thoroughly. Spread crumb mixture over eggplant casserole.
Bake in the preheated oven until casserole is bubbling and crumbs are browned, 35 to 40 minutes.