The Dutchman enjoyed a winning start to his tenure with the Premier League giants in a 7-0 friendly demolition of Los Angeles Galaxy at the Rose Bowl in Pasadena on Wednesday.
United utilised a system of three central defenders in that match, with Antonio Valencia and Luke Shaw deployed as wing-backs.
Jones, an England international centre-back, admits it is a learning curve adjusting to the new formation, having been used to a flat back four, but insists the team is behind Van Gaal's ideas.
"That's the way we set up," Jones said. "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."
With club stalwarts Nemanja Vidic and Rio Ferdinand having departed Old Trafford, Van Gaal is thought to be keen on bolstering his options in defence, with Borussia Dortmund's Mats Hummels and Arsenal's Thomas Vermaelen touted as potential additions.
Jones is hoping he can impress and nail down a regular starting berth.
He added: "Of course, that's ultimately what I want to be doing. We've lost two great defenders in Rio and Nemanja. But that's football and we move on. Everyone is trying to impress."
