If you don't want to use the right-analog stick for your C-Buttons, you can do what I did as a backup. (This will assume PSx controller is used)
All directions mapped to the Digipad (Up is A-up, Left is A-Left, ect). 90% of the N64 games rely on the thumb pad ANYWAY, so you don't need to make up inputs for the digipad if you don't want to. You WILL lose the ability to "walk" properly though. That is where you are seriously doomed.
A is mapped to "X". B is mapped to "[]". Then Map C-up to "/\" and C-down to "O". C-left is "L1". C-right is "R1".
Since select isn't used, I make that the "L" button for N64 games. "L2" becomes the Z button. And lastly the R button is mapped to "R2".
THAT will let you play OoT flawlessly, even on the PSx controllers without analog. You WON'T be able to have the best control in walking/running, but it does work.