Preheat oven to 400º. Place squash, cut side down, on rimmed baking sheet. Pour 1 cup water in bottom of pan, and bake at 400º for 40 to 45 minutes or until squash is tender when pierced with a fork. Remove squash from oven.
Place potatoes in a large pot, and cover with water by 2 inches; add 1 tablespoon sea salt. Bring to a boil over high heat; reduce heat to low, and simmer 20 to 25 minutes or until tender. Drain and place back in pot. When squash is just cool enough to touch, scoop flesh from skin, and add squash to potatoes.
Melt butter in a small sauté pan, and add thyme; simmer about 1 minute. Add butter mixture, pepper, orange juice, sour cream, and remaining 2 teaspoons sea salt to squash and potatoes. Mash until smooth and well blended. Serve warm.