Toilet training little boys
Little boys and okay big boys too often miss the toilet. Urine odors around a toilet can be difficult to treat once it soaks into the flooring. It may be that you will need to replace the flooring around the toilet to get rid of the smell.
Try pouring a fourth of a cup of Nature's Miracle, found at pet stores, on the area. Let it penetrate to the sublayers of the flooring. Nature's Miracle is made from enzymes that "eat" the bacteria causing the odors. It does not mask odors like most chemical treatment, it gets rid of the cause of the odors so they cannot return. If this does not solve the problem, then you will need to refinish or replace the floor.
Here is a trick to help your litte boy hit the toilet. Place a piece of toilet paper flat on top of the toilet bowl water. Have him aim for the sheet to "sink" the boat. Most boys love the game and their aim gets pretty good!