I agree that carrying a pack on a trail is the best training for backpacking. But part of the trick is to understand that walking on a trail is a repetitive activity and therefore subject to repetitive stress injuries. The solution is to not overstress your body during your conditioning hikes/walks. Carry less weight than you will on the AT. Walk fewer miles, especially at first.

Try to get in a variety of terrain, especially uphill and downhill, because these two directions use different sets of muscles. Uneven ground, with rocks and roots, will strengthen your lateral-stabilizing muscles in your knees and ankles. Start slow, see how it feels, and work your way up the ladder of challenges. Injuring yourself is the exact opposite of what you're aiming for, since injuries totally screw up your conditioning schedule and can have long term effects you never heal from.

Above all, listen to your body. Constantly. It knows WAY more about what it needs than your brain does.