The Dutch tactician was brought to Old Trafford after David Moyes' disastrous nine months in the top job, but is yet to reverse United's flagging fortunes.
Van Gaal has deployed a 3-5-2 formation, although he is yet to win a competitive match - with United following up an opening-day loss to Swansea with two draws in the Premier League.
Most notably, however, United were thrashed 4-0 by MK Dons in the League Cup, with alarm bells ringing early in the former Netherlands boss' tenure.
Centre-back Jones, however, insists their new formation is not the problem.
"I personally enjoy the system," Jones, 22, said, as reported by the Manchester Evening News.
"When everyone is working well together and knows what they should be doing on the pitch then it certainly works and is very difficult for teams to play against.
"I think the more we train and play, the more people understand their role on the pitch."
Jones earned his 12th England cap in their 1-0 friendly win over Norway at Wembley on Wednesday, and the former Blackburn Rovers man hopes his club form can assist his international ambitions.
"I hope I can play well for United and, ultimately, nailing down a starting spot [for England] is the aim for anybody that's in the squad," he said.
"Everybody wants to start, but you have to prove yourself first. I hope starting for United under the new manager will help me achieve that.
"I have always said I would like to play at centre-back for both club and country so, hopefully, I can do that."
Jones started and played all 90 minutes of England's 0-0 draw with Costa Rica at the World Cup, which was a dead rubber after Roy Hodgson's men suffered defeat in their first two group games.
"Personally I enjoyed it," he said.
"I enjoyed being at the Euros two years prior to that, but I didn't play and that was disappointing. So to play in a World Cup was great, even though we were already out.
"That was hugely disappointing having been together for so long and trained for the weeks building up to the tournament.
"But playing in a World Cup in Brazil is not something that everyone has on their CV. To wear the England shirt in front of thousands of fans in a World Cup was special."
Jones is set to start in England's opening Euro 2016 qualifier against Switzerland in Basle on Monday.
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