1. Heat oil in large nonstick skillet over medium-high heat. Add onions, and sauté until medium brown, about 10 minutes. Stir in chickpeas, kidney beans, apples, dried fruits, port and honey, and bring to a simmer. Remove from heat. Season with thyme leaves, salt and freshly ground black pepper. (Filling can be made to this point, covered and refrigerated up to 3 days.)
2. Preheat oven to 350°F.
3. Pack squashes with filling, place on baking tray and bake, uncovered, 25 minutes. Cover with lids, and bake 20 to 30 minutes more, until squashes are tender. Garnish with thyme, and serve.