Preheat oven to 375 degrees Fahrenheit. Cook shells in a large pot of boiling water, stirring often, until just tender, about 15 minutes or according to package directions. Drain and rinse under cold water.
Heat oil in a large nonstick skillet over medium-high heat. Add onions and cook, stirring occasionally, until softened, about 3 minutes. Add spinach in batches and toss with tongs until wilted. Poor out excess moisture.
Combine cream cheese, 1/4 cup Parmesan and nutmeg in a bowl; mix well. Add the reserved spinach and season with salt and pepper.
Stuff each of the reserved shells with a generous 2 tablespoons of the ricotta mixture. Spread 1 cup marinara sauce in the bottom of a 9-by-13-inch baking dish. Arrange the stuffed shells in a single layer. Top with the remaining 2 cups of the sauce and sprinkle with the remaining 1/4 cup Parmesan cheese. Bake until the top is golden and the shells are heated through, about 30 minutes. If the top browns too quickly, tent loosely with foil.