I think a good way would be to let the user decide. Give the user some options if you can.
A nice way for my ppc is to use the stylus to move the character. If I tap on the left side of the screen then the character goes left. Or make that tap and hold. And the same when going right. Then using one of the buttons to shoot. Or even better to tap on the character itself to shoot.
I don't know how well that would work, but being able to play the game entirely with the stylus would be a big bonus. That way the user can decide whether to play with the keys, the stylus or even with both.
Have a great time. I look forward to see what you do.