James Collins netted a first-half brace, before Danny Hylton grabbed a third for the visitors in the second half.
Jones opted to change his entire XI at the break, with younger players such as Josh Neufville and Corey Panter getting a run-out alongside first team regulars.
The boss said: “I am pleased. It’s the end of a gruelling week for the players, they have covered a lot of distance and I have seen today as an additional training session. I told the boys that, but within that you want to win the game because you want to create good habits. Touch wood there were no injuries, so all-in-all it has been a really satisfying week.
“I felt like an assessor today, I was assessing what was going on, but I made sure that within the performance there was a priority in winning a football match. We managed to win both halves – second half we kept a clean sheet, so I am delighted.
“Taking charge of a game was nothing different for me – I think I have been a heavily involved assistant manager, I don’t think I have been someone that’s been there for part of the ride. I have done things like this in the past, so it felt very natural and very normal.
“Two centre-forwards scoring three goals between them, that’s what you want. You need your centre-forwards scoring goals. So I am really, really happy, especially after James’ injury, he’s had a full week’s training, he’s not missed anything, so I am pleased.”