pkmom47,
Not sure which service your son is looking to attend. Each one has different body fat standards, and all the body fat standards are an administrative issue (not medical so DoDMERB has no control over them). What will happen, once the form is submitted to admissions, they will figure out the body fat percentage. For this next part I can only speak from a Naval Academy standpoint since I worked with them the most, if your son is over the body fat %, USNA admissions would contact your son and let him know that he needed to drop a certain percentage. Naval Academy does not grant waivers for being over body fat, even for recruited football players, and you must be within body fat by induction day. I'm really not sure how the other service academies work it, and hopefully someone else can shed some light on that aspect.
If your son is over body fat, there are a couple of things he can do that can help decrease the body fat %. First is to lose some in the waist (measured at the bellybutton), second is to gain in the neck (measured just below the adams apple). A one inch drop in the circumference value (neck minus waist) equals a 2% drop in body fat.
At this point in time I would not panic. Submit the form to admissions, give them a couple of weeks to process it, and then give them a call to see where he is concerning the body fat. If the academy wants your son, they will work with him for a while (March usually) before giving his spot away. And I'm sure that the trainers at his school would be more than happy to help him obtain his goal.