for zelda is simple make A and B the usual zelda buttons R for shield like always and the bottom screen to change items, there you go (action in top screen) easy smooth and without problem.
for banjo well i have no idea becuase that game had a deeper control scheme than zelda itself but it could work if you do the same idea as zelda and mario 64
well how about. you equip the items from an item list on the touch screen and you actually use the items (like the fairy sword or arrows) with X and Y, also you can throw the arrows with the touch screen by changing the view from top to bottow
