Preheat oven to 375 degrees. In a mixing bowl, using a fork, blend together Ricotta cheese and egg. Stir in basil, thyme and garlic.
Add 2 cups mozzarella and Parmesan cheese and toss mixture to combine. Mix in prepared spinach. Season mixture with salt and pepper to taste.
Spread 1/3 cup marinara sauce into an even layer along bottom of a 13 by 9-inch baking dish (or similar size casserole dish). Divide cheese mixture among cooked pasta shells, stuffing each shell full with about 2 Tbsp cheese mixture.
Align shells in baking dish side by side, with the opening of shells facing upright.
Stir red pepper flakes to taste into marinara sauce if desired. Cover shells evenly with remaining marinara sauce then sprinkle tops evenly with remaining 1 cup mozzarella cheese.
Cover baking dish with aluminum foil and bake in preheated oven 30 minutes. Serve warm.
*If you don't want to steam fresh spinach, you could also use frozen and thawed spinach, just dry it well by squeezing dry with several layers of paper towels.