Make the meat sauce. Heat olive oil in a large skillet over medium-high heat. Add ground beef and brown without stirring for 1 minute, then break it up and cook for about 5 minutes until fully browned. Add minced garlic and cook for 1 minute. Add diced onion and cook for 6–8 minutes until soft and translucent.
Build the sauce. Stir in tomato paste and cook for 1 minute. Deglaze with red wine, scraping the bottom of the pan, and cook off the alcohol for 2–3 minutes. Add marinara, salt, pepper, thyme, and sugar. Bring to a boil, then reduce to a low simmer uncovered for 40–45 minutes, stirring occasionally. Stir in fresh herbs at the very end. Taste and adjust seasoning.
Make the cheese filling. In a bowl, combine ricotta, egg, parsley, nutmeg, and 1 cup of shredded mozzarella. Mix until smooth and thick. Refrigerate until needed, up to 2 hours.
Prepare the noodles. If using traditional noodles, boil in salted water for 4 minutes only (not fully cooked). Drain, rinse with cold water, and lay flat on oiled parchment paper. Skip this step for oven-ready noodles.
Preheat and prep. Preheat oven to 375°F (190°C). Grease a 9×13 inch baking dish. Spread a thin layer of meat sauce across the bottom.
Assemble the layers. Layer in this order: noodles → meat sauce → shredded mozzarella → ricotta mixture. Repeat twice. Finish with a final layer of noodles, remaining meat sauce, and all remaining mozzarella on top.
Bake covered. Insert 8–12 toothpicks into the top to prevent foil from sticking to the cheese. Cover tightly with aluminum foil. Bake for 30–45 minutes.
Brown the top. Remove foil and broil for 3–5 minutes until the top is golden and bubbling.
Rest before serving. Remove from oven and rest for at least 15 minutes before cutting. This allows the layers to set for clean slices.