Cook bacon in a large nonstick skillet over medium heat until crisp. Remove bacon from pan, reserving 2 teaspoons drippings in pan; crumble bacon. Add onion to drippings in pan; sauté 3 minutes or until tender.
Place potato slices and onion in a 5-quart electric slow cooker coated with cooking spray. Combine 1/2 cup water and next 3 ingredients (through pepper); stir into mixture in slow cooker. Cover and cook on LOW for 8 hours or until potatoes are tender.
Mash mixture with a potato masher; stir in milk and 3/4 cup cheese. Increase heat to HIGH. Cover and cook on HIGH for 20 minutes or until mixture is thoroughly heated. Ladle soup into bowls. Top with sour cream and remaining 1/4 cup cheese. Sprinkle with bacon and chives.