One of the first decisions you have is whether to use a crate. The crate has two main functions. First, it keeps your dog and your possessions safe while you are away, and second, it encourages your dog to inhibit the urge to eliminate.
For example, if you come home and find a puddle of urine on the floor, show it to your dog, and punish your dog (either physically or vocally), your dog will associate the punishment with you and the puddle of urine and not with the act of urinating in the house. This may seem like the same thing to you, but for your dog there is a huge difference between the act of urinating and a puddle of urine.
Since your dog does not understand that it was its act of urinating that contributed to the punishment, it may in the future cower or act guilty when you come home to find another puddle or urine on the floor. Your dog's guilty behavior is merely canine submission and it is its way of telling you that it acknowledges your anger, but does not understand its cause.
In fact, punishing a dog for eliminating inside has been known to lead to other behavioral problems. A classic example is the dog who after repeatedly being punished for eliminating inside, develops coprophagia (the nasty habit of eating feces). In this case, the dog views the feces as the cause of punishment and attempts to get rid of it by eating it. Again, the dog did not understand that its defecating caused the punishment.
Clean any soiled areas with mild soap and an odor eliminator.
If your dog has an accident (and most will have at least one), getting rid of the underlying odor is crucial. Dogs use scent cues when deciding where to eliminate, and the average dog as 215 million more scent receptors than you. Thus, even if you cannot smell that spot on the rug, chances are that your dog can. Never use an ammonia-based product to clean up after your dog. Many of these products just smell too much like urine for your dog to resist. Always place your dog in another room before cleaning up a mess. You do not want this to become a game.
Health and Behavior
If your dog continues to eliminate inside after repeated attempts to house-train or if your house-trained dog begins to eliminate inside, it may have a medical problem or behavioral problem that needs to be addressed. First, have your dog thoroughly examined by your veterinarian (including urinalysis and fecal exam) to rule out any medical problems. If your dog is healthy and the problem persists, ask your veterinarian to refer you to a qualified animal behavior specialist.
An alternate to crate training is to confine your dog to one area of the house using a baby gate or door when left unsupervised. Just make sure that the area is puppy-proof. You can gradually expand its access to the rest of the house. If you use a crate, remember the following: No dog should be crated for more than four consecutive hours! Your dog may still have accidents in the crate. The crate must be large enough for the dog to completely stand up and turn around in, and your ultimate goal is not to use the crate.
Teaching a dog to eliminate indoors, even on paper, makes it more difficult to ultimately teach the dog to eliminate outdoors. If you do not have to paper train your dog, then don't. This said, there are some circumstances when you might want to consider paper training. For example, if your dog is very young or very old and you can not take the dog outside to eliminate as frequently as it needs, you may need to paper train. Small dogs can even be litter box trained. It is possible to house-train a dog that has been paper trained, but it may take more time and vigilance on your part.