man, I just did that scene last Saturday, and boy was it a pain, switching from the button taping to the simon says circles.
First off, don't switch your control set up. A lot of learning how to play is usually getting used to your control set up, so pick ONE that you like, and go with it. Personally I had problems switching my right hand from the arrow key button mashing to the # key pad, especially in putting my finger on 6.
Now is it the button mashing you're having a problem with or the circles? If the circles the only thing I can suggest is practice, but for the button mashing, try using both your hands to tap each button. I used to play the violin and liked to trill, so it's not to hard for me to do it with one hand, but it's just something you have to paractice.