Take the headjoint and body from the case. Without grasping the keys, insert the open end of the headjoint into the wider end of the body (usually closest to the printed brandname of the instrument). The headjoint should be aligned correctly in order to obtain ideal playing posture. In order to do this, the embouchure hole must be aligned with the first key on the body. This refers to the key on which your left index finger belongs. Some flutes has small arrows to indicate correct alignment, in which case, align the arrows.
Next, take the footjoint from the case and connect it to the other end of the body, again, without grasping the mechanism. There is one main rod which is connected parallel to the footjoint. This should be aligned with the last key on the body, approximately in line with the middle of the key. The alignment of the footjoint can be adjusted for greater comfort, depending on the length of your right hand little finger.