The Dutchman enjoyed a winning start to his tenure with the Premier League giants in a 7-0 friendly demolition of LA Galaxy at the Rose Bowl in Pasadena on Wednesday.
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United utilised a system of three central defenders in that match, with Antonio Valencia and Luke Shaw deployed as wing-backs.
And while Jones admits adjusting to the new formation is a learning curve, having been used to a flat back four, he insists the team is behind Van Gaal's ideas.
"That's the way we set up," the England international told reporters. "We played three at the back, with Luke Shaw and Antonio Valencia as wing-backs, and it worked.
"It's a learning process, but we're getting used to it. Day by day, we're getting better and we'll be ready for the start of the season.
"This is the first time I've played three at the back. That's what the gaffer believes in. If he believes in that, then we believe in it as well.
"I don't think it's hard to adjust to. At times, you've got the two wing-backs helping you as well, so, hopefully, it'll be good going forward."