A few answers here. EA-6B1, begin by walking in them until they begin to shape themselves to your feet and get comfortable. Then run in them starting with probably no more than a mile and just slowly increase the distance each week or so. There's no exact formula, just don't push yourself hard in the boots. If you're doing it right, you'll probably not get a workout and you'll feel like a puss for a while. Get your workout in your shoes, use the boots to strengthen the muscles that might cause overuse injuries, particularly the lower leg.
tnutz, on pick-up day, the sergeant instructors told everyone who brought their own boots to put them back in their bags because they weren't allowed to use them. The only boots you can use are the new tan ones that they issue. You can buy some that look exactly the same but they aren't recognized by the Corps yet and they won't let you wear them. They must have the eagle, globe, and anchor on the side and I don't believe anyone sells those yet.