Louis van Gaal has adopted a back three since taking the reins at Old Trafford in July, though fans and pundits are not completely convinced by the system.
United's defensive frailties were highlighted during Sunday's disappointing 1-0 loss at home to Southampton, which has led to calls for a switch to a four-man defensive system.
But Jones, who makes up part of the three-man backline, is confident United has what it takes to master the formation.
"I think we are comfortable playing in it. Whether we have a back-four or three we are comfortable with both," said the 22-year-old.
"Sometimes maybe we play that pass in the defence that we shouldn't but we are comfortable playing in both formations the manager has shown.
"We are still improving as a team. It's a learning curve. It doesn't just happen overnight. You don't just click your fingers and you are used to playing in a new formation. It's like anything, it takes time.
"But we are improving in training and we want to get better. That's the main thing. Every one of us in the changing room wants to get better, to learn and that's only good for us."
United sit fourth in the Premier League standings ahead of Saturday's trip to QPR.
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