Puppy pads are a useful tool, even for housetrained dogs. While some owners use pads only during training, leaving a pad out 24-7 can prevent the occasional accident. Still, they aren't a "get out of jail free" card, and some cleanup is involved when you replace them.
Remove a soiled puppy pad as soon as you see that it has been used and throw it away.
Spray the floor underneath the pad with a disinfectant spray and wipe it with a paper towel. While puppy pads are designed to not soak through, moisture and bacteria sometimes form underneath a used pad, and it's better to play it safe.
Replace the pad with a new, clean one, and always leave it in the same spot. The puppy pad should be in an area where the dog feels comfortable going—ideally someplace relatively private, and away from his food and water. Keeping the pad in the same place is crucial to making sure that he uses it consistently, so don't go moving it around unless you need to. If you do change the location of the pad, always show your dog where he can find it.