In October 1998, Blackwell found himself making headlines from an incident that had happened during his time at Huddersfield. He was taken to court by the family of a girl whose arm was broken by one of his stray shots during the warm-up. Soon after Torquay chairman Mike Bateson banned his own players from shooting at the goals during the pre-match warm up and the case was delayed so an out of court settlement could be reached. In December 1999, Neil Warnock was appointed manager of Sheffield United and took Blackwell with him as his assistant. In September 2000, Blackwell's thoughts were turned to playing again, he was still registered as a player and due to injuries was the only cover for the Blades' first choice keeper. In August 2014 Blackwell was reunited with Neil Warnock at Crystal Palace. Working together for the first time in eleven years, Blackwell being appointed a Technical Director. Blackwell was asked to continue his role after Warnock had departed until the appointment of Alan Pardew. In February 2015 Blackwell started coaching at Barnet, helping Martin Allen with the Bees' title push in the Conference Premier until the end of the season. In November 2015 Blackwell was brought in by Warnock, then interim manager at Queens Park Rangers, to assist him at the club. In February 2016, Blackwell was appointed assistant manager to Warnock at Rotherham United along with Ronnie Jepson. The management team left Rotherham in May of the same year, having guided the club to safety in the Championship. In October 2016, Blackwell again teamed up with Warnock and Jepson, as assistant manager at Cardiff City. Blackwell left Sheffield United for Leeds United to join Peter Reid as his Assistant Manager in 2003. He remained in this role under Eddie Gray following Reid's dismissal before taking over as manager of Leeds in the summer 2004 following the club's relegation from the Premiership. Handed the task of rebuilding Leeds' team after huge debts forced the jettisoning of its highly paid stars, Blackwell made a record number of signings for the club in 2004–05. He focused on value for money, buying players that, while talented, had not made the highest grade. Although early results were poor, perhaps affected by boardroom turmoil that saw the new board struggle to put the club onto a sound financial footing and in time led to its takeover by Ken Bates, Blackwell led the side to challenge for the playoffs, before a run of draws slowed progress, leaving Leeds in mid-table. Blackwell had been seen as a temporary appointment, perhaps to be replaced by a more glamorous name, but his success in stabilising the team – and his initial popularity with fans – led Bates to suggest he had a long-term future at the club.