After a disappointing start (0–6–0) to the 2007–08 Atlanta Thrashers season, Waddell was named interim head coach of the team following the dismissal of Bob Hartley.

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.

After leaving Orlando, Waddell served as assistant general manager of the Detroit Red Wings in the 1997–98 season, capturing the Stanley Cup.

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.

[3] Waddell left the Penguins organization on July 1, 2014, to become the president of Gale Force Sports & Entertainment, the parent company of the NHL's Carolina Hurricanes.

[6] On May 28, 2024, Waddell was named president of hockey operations, general manager and alternate governor of the Columbus Blue Jackets.