I am using a controller as well, I placed the mudras on my 2nd crosshotbar right side. B (Ten) A (Chi) X (Jin), Y is Kassatsu, while Y in 1st crosshotbar is Ninjitsu, I found that this works better for me.
Once setup is more in remembering which direction to press the buttons and the final mudra for the Ninjitsu you want to use.

B > A is Raiton, go opposite is Katon
B > A > X is Suiton go opposite is Huton
X > B > A is Doton
A > X is Hyoton

I am only remembering the direction to press rather than what I have on the buttons, as this is faster and I do not have to look at the crosshotbar much.