I did apply to all three academies. For me, West Point was initially #1 and USAFA was #2, followed by Annapolis. However, I went out for a trip to USAFA and it completely changed my mind. In addition, I had an Army liaison who didn't exactly inspire me to go the Army route. I remember those days of interviews with congressional staff members and fitness tests and letters and essays and everything else. Good luck to your boy. May he find the best situation for him.
As for the additional nominations, I remember getting a letter from Senator Hatch that said something to the effect of "I would normally give you a nomination, but you already have a nomination and there is no sense in giving you two nominations when I can nominate another Utah resident." He was very complimentary in the letter, but it made me mad because I wanted a stack of nominations