Ferguson believes both players are best suited in the typical No10 role.
"Good footballers can play together. But I think the preferred position for Shinji is off the front man in a central position, and that's the same for Wazza [Rooney's nickname]. We maybe have to alternate them.
"Shinji likes to play through the middle on his own. He played there last week for 20 minutes against Norwich, made two goals and scored one. Van Persie is in strong form and we had to leave out Chicharito [Javier Hernandez] because of Van Persie. It's not easy.
"At Newcastle we played a diamond and that's a consideration. We played Wazza centre midfield and Shinji towards the right. They did really well in that game."