The body is aligned along the chakras in the same manner as your physical extremities. For ailments on your right side, you would use your right foot to apply pressure.
For ailments that seem to be centralized, you would apply pressure to both feet. Either simultaneously or starting with your predominate side. If you're right handed, start on the right, for example.
Some practioners further suggest, that an overall treatment starting at the base chakras and moving upwards, can help to keep an individual in balance and good health.
To locate an area of your body to work with, think of your feet as a map of your body. Starting at the head, you're toes, and moving down to the heal for your foot. These two diagrams depict (within reason), the inner workings of your body as they would appear within your foot You should note the slight differences between the right side and left side of your feet as well. After all, not all your organs are in the exact center of you body.
The major differences are in the mid-sections of the body, which equate to the arches of your foot.
On the right, you'll find your Stomach, Adrenals, Pancreas and Duodenal. While on the left, look for your heart, spleen, kidney and waist.
An area such as the Spine, between the shoulders will exist on both feet, but if you feel discomfort on one side over the other, then concentrate on that foot. Otherwise, it would be appropriate to perform a session on both feet.
Source: Pagans Path