It's one of the unique aspects of working with a middle school or high school youth choir and it's a process - one that takes understanding, patience, and flexibility.
Voice change occurs during adolescence when the larynx and vocal cords lengthen and thicken (source). For boys, the change is dramatic; for girls, more subtle. However, it is important to recognize the changes that occur in all voices and ways to encourage and support singers throughout the process (and keep them singing!).
Encouragement is vital to the process. Do what you can to make singers feel comfortable experimenting and trying things, help them learn how to be flexible and support one another throughout the process.