Sort and wash pinto beans; place in a large Dutch oven. Cover with water to 2 inches above beans; cover and let stand 8 hours. Drain beans. Combine beans and 4 cups water in pan; bring to a boil. Reduce heat, and simmer 30 minutes. Cover and simmer 30 minutes or until tender.
Heat oil in a large nonstick skillet over medium heat. Add onion, squash, carrot, and chile; cook 10 minutes, stirring frequently. Add to bean mixture. Stir in sage, thyme, and tomatoes; bring to a boil. Cover, reduce heat, and simmer 10 minutes or until squash is tender. Stir in salt. Ladle stew into individual bowls; sprinkle with pumpkinseed kernels.