You can use an iCade controller with this emulator
There are 3 that I know of. The 8-bitty, iCade mobile, and Gametel. I'd personally recommend the Gametel as the 8-bitty doesn't hold your phone so portability is lacking, and the iCade mobile is a bit bulky for me. The Gametel is both compact and can clip your iPhone in place to take it on the go like a real game console instead I having to place your phone on the table.
Just know that on any iCade controller you use the button layout is kind of wonky. By this I mean that the d-pad works fine, but on LoZ: ALTTP the attack button is the upper left shoulder button and the button to pick things up is the start button. Can be awkward at first but you get used to it