Preheat oven to 325 degrees. Season capon pieces with salt and pepper, reserving back and wings for another use. Spread matzo meal in a shallow dish, and season with salt and pepper. Dredge capon in matzo meal, tapping off excess.
In a large Dutch oven over medium-high heat, melt 2 tablespoons margarine. Working in batches so as not to crowd the pan, sear the capon until golden, about 4 minutes per side. As each batch is finished, set aside on a platter. Add more margarine to the pot as needed. When all capon pieces are browned, pour off excess fat.
Add the wine, and cook scraping up any browned bits from the bottom of the pan, for 2 minutes. Add the capon and onions. Scatter the thyme over the top, and stir in the stock. Bring to a boil. Cover, and transfer to the oven. Bake until capon is tender, and cooked through, about 1 hour. Remove from oven.
Using a slotted spoon, remove the capon and onions to a bowl; cover and keep warm. Alternatively, you may store the capon and onions in an airtight container in the refrigerator up to 2 days. Store the sauce in separate container. Remove thyme sprigs and discard. Place Dutch oven over medium-high heat and cook, skimming fat and foam as necessary, until reduced and slightly thickened, about 15 minutes. Return the capon and onions to the pot and heat through.