Jones moved to United from Rovers in the summer.
Bowyer told the Daily Mail: "Phil arrived at the academy as a goalscoring outside right after being spotted in a local kids' cup final. We moved him to central midfield, then to centre half - and that's where he began to make his mark for the Under 16s and 18s.
"I've heard people say he didn't necessarily look head and shoulders above everyone else and I can see what they mean. He did really well in his first year after being taken on full time, but not quite so well in a couple of games after that.
"In fact, we left him out after a couple of mistakes in a youth team game at Nottingham Forest. There was a stray back pass that went straight to one of their players and he was out of position for another of their goals. It's a measure of his determination to put things right, though, that he was making his first-team debut in the Carling Cup within a year."