I agree with bandit that fares on the discount sites are usually less that the military discount.
Here is our system for booking flights with our cadet, and it has worked very well for us:
We have an Orbitz account that both our son and we can access. Our cadet goes online when he knows his schedule and books his own flights. That way there is no miscommunication about the whens and wheres of his flights. The Orbitz system allows you to have several credit card profiles on the account. We have an agreement that we pay for three trips home per year, so when he books one of those trips he uses our credit card. We can look on the account and get the flight numbers and times without having to bug him about it. He also has his own card on file, so when he makes an extra trip home or flies to see his girlfriend, he pays for those flights. This system has been great for us because it gives him the responsibility of booking flights that work for him, and also lets us pay for some of his trips home. It's just a suggestion, but it has worked well for three years for this family.
Stealth_81