The Dutchman's first game at the helm saw United adopt a 3-5-2 formation for a crushing 7-0 victory over Los Angeles Galaxy.
Van Gaal's theory is that by fielding three centre-halves and wing-backs, he is then able to go with two out-and-out strikers.
The move represents a significant change for a club that has long favoured a flat back four but Jones, one of those forced to adapt quickly as part of the new defensive unit, feels tactical tinkering could benefit United in the long run.
The versatile England international 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 that 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."
Jones is also hoping that the 2014/15 campaign will see him nail down a regular starting berth at Old Trafford, with the summer departures of experienced heads such as Rio Ferdinand and Nemanja Vidic paving the way for the next generation to step up.
The 22-year-old 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."