Add the olive oil to a large pan over medium heat. When hot, add the red onions and saute just until soft, not browned; add the garlic. If you'd like to make the sauce spicier, add a pinch red pepper. Add the tomatoes and sprinkle with salt and pepper.
Simmer over a medium-low flame for about 30 minutes. Strive for balance in the consistency of the sauce; it has to be fluid but it shouldn't look overly wet. A few minutes before taking the sauce off the fire, season with salt and pepper.
Preheat the oven to 350 degrees F.
Add the Swiss chard to the pan with the red sauce; toss, and cook for about 3 minutes, until tender.
Meanwhile, bring a large pot of salted water to a boil. Cook the fusilli according to the directions on the box, and, as always, to make sure you achieve a proper "al dente" texture, drain it about 2 minutes before what is indicated. The pasta will cook again in the oven, so you do not want it mushy.
Toss the pasta and the sauce together, season with salt and pepper, and toss in three-quarters of the mozzarella and pecorino. Divide between eight oiled 10-ounce ramekins. Top each with a light sprinkling of the cheeses.
Bake in the oven until golden and crisp on top, about 15 minutes.