x/y switching has the same implementation as effect bypasses. That is (from memory) sending a CC value 0 selects X, sending 127 selects Y (more specifically I think it's actually 0-63 = X, 64-127 = Y). Everything you need to know is in the Axefx manual.
So on the GT you just need 1 IA button. Use the 'select cc' feature in the GT to find which x/y you want and it should be all set up. When the button is off it should be in X, when it's on it should go to Y.