Place the squash, cut sides down, in a glass baking dish. Place the baking dish into the oven and pour enough water into the baking sheet to fill halfway up the sides (this will help steam the squash so it doesn't dry out, making the flesh easier to mash). Place the foil-wrapped garlic directly on an oven rack. Roast the garlic and squash until very tender, about 1 hour. Cool slightly.
Melt 1 tablespoon of butter in a heavy, small skillet over medium-high heat. Add the leeks and apple and saute until crisp tender, about 6 minutes. Season with salt, to taste.
Scoop the cooled acorn squash flesh into a large bowl. Using a potato masher, mash the flesh until smooth. Unwrap the garlic and squeeze the roasted garlic flesh into the squash puree. Add the remaining 6 tablespoons of butter and mash. Stir in the thyme and season with salt, to taste. Place the mash in serving bowl and top with apple and leek saute.