You have probably seen and heard many different ways to align your head while in the three-point stance. Some coaches want you to keep your head down and looking back at your legs at the start. Other coaches believe that you should have your head up so that your eyes are looking forward. This may work on the football field since you need to see the ball snapped and know what's happening on the field, but we are looking to your body in the best 'exiting' position possible.
Your head position should be properly aligned with your spine (so it is straight). Looking down and back normally causes the athlete to break at the hips while driving out while trying to maintain that position. Also, another problem that I have seen with trying to keep the head down is that it can cause the athlete to lean too far forward while in the starting position and it causes a breaking of the hips in the drive phase.
Hips should be above the shoulders. The degree of height above the shoulder will affect knee and hip angles, thus affecting force application and acceleration. The higher your hips the more weight you can shift to the hands.
Make sure that your hips aren't too high or you won't be able to support all the weight and your first step off of the starting line will be short--almost "catching" your body from falling. If your hips are too low, you could have too much weight back where your body can't explode as ideally as you would like to overcome inertia. Also, you are most likely to 'pop' straight up on your first step, negating your acceleration phase.
Hands should be placed about shoulder width apart to start. The hands should also be arched, so that only the fingertips are actually touching the ground. Doing this ensures that you will not place too much weight on your arms which forces your legs to move the majority of your body's mass. The thumb and index finger are going to take on the majority of the weight. They will also run parallel with the starting line.
Your quick side hand is going to be the hand that is going to be left on the ground supporting during the set position. Your power side hand will be raised off of the ground. Keep the power side arm at 90 degrees with that hand by your hip. Keeping your power side arm at 90 degrees at the starting position will enable you to come through with that arm quickly when driving out. The biggest reason to keep that arm at 90 degrees at the starting position is if your 40-yard time is being timed by a stopwatch and not electronically.
If someone is manually timing your 40 with a stopwatch, they are going on your first movement. If your power side arm is up to 120 degrees or so, it is easier to see that arm move first and it won't be as noticeable if it is kept at 90 degrees. So, it might be slight time saver, but as you know, every little bit helps.
Most football combines time their 40-yard runs electronically. One of the easiest ways for them to time is to have the electronic timing device connected to a gun, when the gun fires, the timing starts. So, here is a tip if you are getting your 40 timed by your reaction to the gun.
There are two things you can focus on. One is to focus on a motor set, which means to focus on your first movement, not the gun. Second, would be a sensory set. This means that you would focus your attention on the starter's gun. Focusing on the gun isn't necessary because you are going to hear it and react to it whether you are focusing on it or not.
By focusing on a sensory set as opposed to a motor set, you are likely to get a slower reaction time to the gun. By waiting to react to the gun, you have to wait to hear the gun, and then your brain has to acknowledge the sound of the gun, and then send a signal to your muscles to react to the gun. This might only take .10, but it is time you cannot afford to waste. Instead, you should focus on driving the power side arm (if your right leg is forward, then drive your right arm) up as soon as the gun goes off. This will help bring your quick side leg through as well as help you drive through your power side leg.