He could very well be suffering from plantar fasciitis, which is an inflammation of the plantar (the hard tendon that runs from the ball of the foot to the heel and forms the arch). I have very high arches and suffered with heel pain through much of my childhood and still suffer from left foot ball pain from the same condition.
Heel cups do help, but this condition takes months to heal. It's not going to resolve quickly, no matter what you do, and bear in mind that any sort of cup or orthotic should be worn in all of his shoes -- not just his soccer shoes -- since you are trying to calm a condition that is exacerbated whenever he is on his feet.
If he's flat-footed, the arch supports could be compounding the problem since they're trying to put more of an arch in his foot than his physiology has provided for. My husband and several of my family members are flat-footed and their foot pain is increased with the use of orthotics.
You could consider one of the custom-molded orthotics such as what is offered through the "Good Feet" store. In this, they take a mold of the foot and custom make the support to fit your foot's natural terrain. I understand that this is an excellent, albeit expensive, solution for many. Their supports are reputed to be well made and last for a long time.
Finally, I make therapeutic salts that would make an excellent foot soak for him in the evening ... particularly after a practice or game. My Gingergrass salts are great for detoxing through the feet, so if his soreness is connected to any toxic buildup in his body, it will help eliminate it. My Bergamot salts are excellent for athletes as they help to prevent or correct foot odor and fungal infections often experienced from exertion while wearing closed in shoes.
Take a look at my website: www.mccluckfarms.com or write me for more info.
Best of luck!