Manners made his directorial debut in 1978, directing an episode of Charlie's Angels. Prior to this, he had worked as unit production manager on the show and as an assistant Director on a handful of other projects. Other notable directorial credits to Manners' name include episodes of 21 Jump Street, Mission: Impossible, Star Trek: The Next Generation, Baywatch, K-9000, and The Commish.
Manners left his directing job at Stephen J. Cannell Productions in 1993 to work on the television series The Adventures of Brisco County, Jr. He directed 7 of the series' 27 episodes, more than any other Director for the show. He joked that he was the series' "mascot director". He was happy with the work for the series, and felt that it "stretched" him creatively. He said, "It really woke me up as a Director, almost spiritually…" and that directing for Brisco was a large contributing factor to his later success as a regular Director on The X-Files.
Manners, along with his fellow producers on The X-Files, was nominated for four Emmy Awards for Outstanding Drama Series in 1995, 1996, 1997 and 1998. Manners was referenced in the X-Files episode "Jose Chung's From Outer Space" with a foul-mouthed police detective named after him. Following the finale of The X-Files in 2002, Manners directed a number of small projects before signing on to direct and produce Supernatural in 2005.
The closing credits of the Supernatural season four episode "Death Takes a Holiday", which aired on March 12, 2009, showed two photos of Manners, along with the caption "We dedicate the entire season to Kim Manners" and a message stating, "We miss you, Kim." The fifth episode of the second season of AMC's Breaking Bad, titled "Breakage", which premiered on April 5, 2009, featured a dedication to Manners in the end credits, which stated "Dedicated to our Friend, Kim Manners". The episode "Mulder and Scully Meet the Were-Monster", from the revival season for The X Files which aired on February 1, 2016, features a scene where Mulder sits against Manners' gravestone, inscribed with Manners' real date of birth and death, and the phrase, "Let's Kick It in the Ass."
