To make things worse, dogs will tend to return to an area they've already soiled, so the smells in your house may be making housetraining even harder than it already is. The good news is, there are products that can help reduce dog odors, depending on what kind of surface you are dealing with. If you are trying to clean unsealed concrete floors, like those you might find in the garage or an unfinished basement, the urine may have seeped in and absorbed. You will need to clean with a disinfectant and allow the disinfectant to sit and seep into the floor. Once you've rinsed with water and allowed the floor to dry completely, you'll want to seal it so that liquids won't be absorbed in the future.
Concrete sealant is widely available at hardware stores.
Linoleum and sealed concrete floors can be cleaned with disinfectants that you can purchase from your veterinarian. You can then clean the carpet with an enzymatic cleaner, available from professional carpet cleaners. Once you've cleaned the odors out of your floor, your best option is prevention. You may want to consider crate training for your puppy. Crate training gives you control over where and when he is eliminating, and it often housetrains dogs quickly and effectively.