I only tried using a gamepad very briefly, but IIRC by default you have two hotbars - one assigned to L2 and one to R2? Your four cross/square/circle/triangle buttons are the easiest to use, so bind your key skills to them, and I'd probably find R2 easier to use alot. I'd experiment with something along the lines of:
R2 hotbar:
cross - Cure
square - Regen (when you get it)
circle - Stone / Stone II (at least while you're leveling, maybe you'll want to rebind this later. Keep it handy as you'll use it a lot.)
triangle - Cure II
up - Aero
right - Thunder
left - Protect
down - Fluid Aura
L2 hotbar:
cross - Medica / Medica II
square - Stoneskin
circle - Stone (once you have Stone II)
triangle - Benediction
up - Cleric Stance
right - Divine Seal
left - Shroud of Saints
down - Swiftcast + Raise macro
That's based on speculation off the top of my head, so you'll probably be able to improve it through experience, but it's based on basic ideas that seem sensible:
-if you use something a lot, it should be accessible;
-buttons should have similar uses on hotbars (circle=attack, square=buff, cross=heal, triangle=big heal, arrows=occasional use skills, stances).
I'm sure you'll be able to improve that a lot by introducing more hotbars, but I'm not familiar enoug hwith using a gamepad to say anything about that.
