Preheat oven to 425 degrees F; scrub potatoes and prick with a fork.
Place potatoes on a foil lined baking sheet and bake until tender, about 40 minutes, remove from oven and let cool slightly; reduce oven temperature to 325 degrees F.
Once potatoes are cool enough to handle, scrape pulp from skins into a bowl and mash; add 2 tablespoons butter, 3/4 teaspoon salt, stir in cheese,bourbon (or juice), cream, and 2 tablespoons of the brown sugar while mashing.
Transfer to a buttered 1 1/2 quart casserole; cover, bake until heated through, about 30 minutes.
Meanwhile, in a microwave safe 2 quart casserole, combine remaining butter, brown sugar, and salt; add onions.
Microwave on high until onion is crisp tender, about 3 to 4 minutes; add apples, cover and microwave until apple is tender, 2 minutes more.
Stir in thyme and pepper; serve with sweet potatoes.