After his tenure as a player, he moved to coaching for the 1987–88 season with the IHL Flint Spirits as a player-coach. For the next two seasons, he moved behind the bench permanently. Waddell moved on to the IHL San Diego Gulls for the 1991–92 season. Waddell took over as interim coach of the Atlanta Thrashers during the 2002–03 season with a record of 4–5–1–0 as coach before Bob Hartley was named to the permanent job. After a disappointing start to the 2007–08 Atlanta Thrashers season, Waddell was named interim head coach of the team following the dismissal of Bob Hartley. For several months, he was able to lead the team on a turn around, but the Thrashers ultimately played poorly down the stretch and missed the playoffs.
Coaching record
Management career
Early career
Waddell's first front office experience came with the International Hockey League's Flint Spirits during the 1988–89 season when he served in the dual role of head coach and general manager. He moved into Flint's front office exclusively for the 1989–90 season before joining the IHL's San Diego Gulls. He was vice president and general manager for the Gulls from 1990 to 1995 before accepting the same role with the IHL's Orlando Solar Bears. While in Orlando, Waddell was also vice president of RDV Sports and served on the organization's executive committee which oversaw the NBA's Orlando Magic, the Solar Bears and RDV Sports' retail and aviation interests.
On June 23, 1998, just one week after the Red Wings swept the Washington Capitals in the 1998 Stanley Cup Finals, Waddell was named the first general manager of the Atlanta Thrashers. He served as general manager of the Thrashers until the conclusion of the 2009–10 season when he was promoted to team president, and Rick Dudley succeeded him as general manager. During his tenure as general manager of the Thrashers, the team recorded a 308–401–45–66 record and made their lone playoff appearance after winning the NHL's Southeast Division in 2006–07. Waddell also served as executive vice president and co-chair of the executive committee for the Thrashers' parent company, Atlanta Spirit. Following True North's purchase of the Thrashers, Waddell announced he would not be moving with the team from Atlanta to Winnipeg.
On January 21, 2012, the Pittsburgh Penguins announced their hiring of Waddell as a professional scout.
Carolina Hurricanes
Waddell was named President of Gale Force Sports & Entertainment, the parent company of the NHL's Carolina Hurricanes, on July 1, 2014. On May 8, 2018, Waddell was named president and general manager of the Hurricanes.