Pros and Cons of Puppy Pads when Potty Training?

My pup is 12 weeks old and he is doing great letting us know when he needs to go out not messing at night or if we aren't home for a couple hours. I think puppy pads have confused him though, because he thinks carpets/rugs are okay to use and even looks up for a treat when he uses them. We don't have a doggy door, so I want him to be comfortable using the pads if we aren't home. Looking to hear what others do for those circumstances or how you break the rug/carpet confusion.