Like most things, just practice. Keep in mind that it is not like a "normal" throw, but rather one where you need to get torque out of your hips and midsection. My son found it to work best when he turned his body a bit, so his knees where not lined up evenly. As long as they are both behind the line you are OK. Also try getting either more height or less, until you find your sweet spot. We practiced the CFA on the weekends for several weeks at the high school, and my son made significant improvements in everything except the shuttle run, where he improved only a little, and was just a touch better than average on that. With everything else in the CFA, a reasonably fit kid can work on and make huge strides.
There is always a debate about the importance of the CFA, and getting good numbers there. Many will tell you that it is a "pass/fail", and that is true in the sense that you just need to pass it minimally to meet the fitness "qualification". However, the CFA is also part of the WCS, and the better you do on it, the more points you get. It is worth 10% of the total WCS, I believe, which may seem insignificant in the larger scheme of things, but it is only a few points which separates those qualified candidates who get in and those who don't. Then, when you figure that so many of the WCS points are somewhat fixed by the time a kid applies to the academy, and cant really be changed much, the point generating factors which CAN be improved upon become more relevant. They include the CFA and the ACT/SAT. So work hard and put yourself in the best position possible. Leave no stone unturned.