I had the same thing happen to me as a little one like your son. I eventually outgrew the canker cores (after high school, when hormones leveled out).
I basically just used Anbesol from a small child onward. You could ask the doctor or dentist for a Xylocaine gel to numb the areas for him (this is sometimes used to swab on strep throat). There really wasn't anything to make the sore progress faster. I did notice that if I didn't drink orange juice or other acidic beverages / food, that I didn't get them as much. Also, being out in the sun brought on more sores as well.
There is a distinction between cold sores and canker sores, however. Is your doctor positive that he has cold sores, as he may simply have canker sores. Maybe you can determine this by reading below:
Canker sores are small sores or ulcers that appear inside the mouth. They are painful, self-healing, and can recur. Canker sores occur on the inside of the mouth, usually on the inside of the lips, cheeks, and/or soft palate. They can also occur on the tongue and in the throat. Often, several canker sores will appear at the same time and may be grouped in clusters. Canker sores appear as a whitish, round area with a red border. The sores are painful and sensitive to touch. The average canker sore is about one-quarter inch in size, although they can occasionally be larger. Canker sores are not infectious.
Canker sores are sometimes confused with cold sores. Cold sores are caused by herpes simplex virus. This disease, also known as oral herpes or fever blisters, can occur anywhere on the body. Most commonly, herpes infection occurs on the outside of the lips and the gums, and much less frequently on the inside the mouth. Cold sores are infectious.
The exact cause of canker sores is uncertain, however, they seem to be related to a localized immune reaction. Other proposed causes for this disease are trauma to the affected areas from toothbrush scrapes, stress, hormones, and food allergies. Canker sores tend to appear in response to stress. The initial symptom is a tingling or mildly painful itching sensation in the area where the sore will appear. After one to several days, a small red swelling appears. The sore is round, and is a whitish color with a grayish colored center. Usually, there is a red ring of inflammation surrounding the sore. The main symptom is pain. Canker sores can be very painful, especially if they are touched repeatedly, e.g., by the tongue. They last for one to two weeks.
Canker sores are diagnosed by observation of the blister. A distinction between canker sores and cold sores must be made because cold sores are infectious and the herpes infection can be transmitted to other people. The two sores can usually be distinguished visually and there are specific diagnostic tests for herpes infection.
Since canker sores heal by themselves, treatment is not usually necessary. Pain relief remedies, such as topical anesthetics, may be used to reduce the pain of the sores. The use of corticosteroid ointments sometimes speeds healing. Avoidance of spicy or acidic foods can help reduce the pain associated with canker sore.
I hope this helps... let me know how your son is doing. I feel his pain :*(