What did the NYC cabby tell his passenger when he asked how to get to Carnige Hall? "practice, practice, practice".
If your throwing mechanics are good and you are consistent with how you grip the baseball, your body will make the adjustment to start hitting the target your aiming at. For now I'd just suggest you aim higher.
Try playing catch and long toss with your CU grip. The more throws you make with that grip the more natural it will become.