All to often I see young flute students with improper hand positions when assembling or playing the flute. Some examples may be that left pinky hanging below that G# key or that students are gripping the key mechanism to put their flutes together. These things are not only bad habits, but they may lead to injury of the flute or (more importantly) yourself.
When putting together a flute, it is important to realize that the mechanism is the most delicate part of the flute; gripping it may cause it to bend and force keys out of alignment. So, just how do you do it? Pick up your head joint (mouth end) and the neck of the body joint. The neck of the body joint has a nice open spot for you to grip in your hand. Slowly put the head joint into the body joint and gently turn it in back and forth until the head joint is securely in the body joint. Most players should align the far side of the hole of the mouthpiece to the center of the keys of the body joint, but some may play better with the middle of the mouthpiece hole aligned with the center of the keys. Next pick up the foot joint by its very end, it has a little space between the last key and the hole opening. Still holding onto the neck of the body and the end of the foot, turn the foot joint back and forth into the body; the bar of the foot joint mechanism should align with the center of the body joint keys. You have now properly assembled the flute. Follow the same process when cleaning and putting it away.
Since gripping the flute by the mechanism can be very damaging and very expensive to realign there is one other thing to keep in mind. When you are just holding your assembled flute, maybe in between playing, hold it by the neck of the body. This allows enough space to avoid gripping the mechanism while also having little risk of joints disconnecting.
Flute can be a difficult instrument to handle when playing; it includes three points where the flute rests or balances on your body, your right thumb, the base of your left index finger, and your chin. If the flute is nicely balanced, it should not move or roll around, even when you lift your fingers up to play a C#. Some people choose to have the flute rest on their right thumb, others choose to slightly push with the right thumb so that the head joint presses more into the chin. Whatever choice you make, it should free up the fingers on your right hand so they can quickly press and release their keys. The base knuckle of your left index finger should be the resting point of your left hand near the neck of the body. Both hands should form a “c-shape” when resting on or slightly above the keys, however, your left “c” should face toward you and your right “c” should face away from you. If you experience any discomfort in your fingers, hand, or wrist, make minor adjustments to your resting points on the flute until you feel the most comfort. The pads of your fingers (the fleshy part) should land on the center of the keys when pressing down; however, some have a hard time reaching the G key in their left hand. That is okay, but if you have an open hole flute, you need to have a plug for the holes you have a hard time covering. The left pinky that plays the G# key on flute and should never fall below the key when you are not playing. Try thinking of holding a cup or glass with your pinky raised; keeping your pinky raised for the G# key has a similar feeling. Finally, the lip plate of the head joint should rest on your chin with your lower lip resting on the lip plate.
On a final note, playing your instrument until your fingers, hands, wrists, or shoulders hurt is very harmful to your body (I am speaking from experience). I would suggest that you practice at twenty minute intervals with five minutes in between, where you stretch and relax your hands.