My son was sentenced to 6 years in Colorado's Youthful Offender System (YOS) in June 2016. Will he have to serve the full 6 years or will he be released in 3 years? Also, does it matter if we are not Colorado residents?

Six years is a serious sentence for a juvenile. Depending on the previous criminal history the judge could put an early release provision in the youth's Judgement and Commitment Order. Then, it's up to your son to take the programming "to heart" which would give him a shot at getting out early. If it's available to him and he wakes up, he will more than likely get out sooner than the six years.