I just memorized all of the Ninjutsu's Mudra. Not exactly the names of what order, but the order of which I hit the Mudra to execute whatever Ninjutsu I'm trying to do.

On a controller it may be a bit harder, but to me, the best way to do it is just familiarize yourself with the order you execute them in, and as many have said, never double tap, or double whatever you'd do for the controller. UI delay and lag can easily ruin your Ninjutsu if you do.