He started his coaching career at NCAA Division I Indiana University/Purdue-University-Ft. Wayne (IPFW). He was the director of basketball operations for three seasons and the interim assistant coach for one season. When he was the interim assistant coach, he help guide the team to a then school record NCAA Division I 10 wins. IPFW became a certified NCAA Division I program in 2005 after their four-year provisional period.

Moving onto the NCAA Division III level, Cotton then became the assistant coach for the Anderson University men's basketball team. His three seasons there led to success for the team. In 2007-08, the team finished second in the HCAC and then last year they had the longest winning streak at Anderson in 27 years. In the last two years at Anderson, they won 15 games each and had back-to-back winning seasons for the first time in five years.

His efforts in recruiting have been noted at each stop with the players he has brought in. At IPFW, the team won a then school record NCAA Division I 10 games. At Anderson, he recruited two top 40 seniors from the state of Indiana as well as the seventh leading scorer in the junior college ranks in division II.