A head injury to Daley Blind in the first half of United's 3-1 win over the Premier League saw Rooney switch to a holding position, even deeper than the midfield role he has played much of the season in.
Used primarily as a forward throughout his career so far, Rooney's withdrawn position under Van Gaal has led to criticism by some, who feel the England captain is not being used in his most effective position, but Van Gaal does not agree.
"I have to look for the better balance and I think until now because of Rooney we have a better balance in midfield," he said.
"I was very pleased how he replaced Daley Blind in the number six position.
"He showed composure and of course he was also today the Rooney that I want to see but he has showed that he can play in every position.
"Maybe he can better play in a striker's position but then I have a problem in midfield."
Van Gaal also provided an update on the fitness of Blind and Phil Jones, who was taken off early on and replaced by Chris Smalling.
"Blind has a headache but I don't think he is out of the game on Monday [in the FA Cup against Preston North End]," he told MUTV.
"I think, for Jones, we have to wait. I think it shall be difficult as he was very disappointed when I spoke with him. Maybe it's a knee problem so it's not good."
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