With the intruction of sticks into console controllers i initially struggled as i prefered a "south paw" setup to movement and aiming, (Aim with left, move with right) however at the time few games actually supported that and switching back and forth between setups was ackward, muscle memory being what it is. eventually i sat myself down in front of a shooter, (Halo 2 i believe) and just forced myself to get accustom to the setup. Eventually it become normal for me.
On the PC i have my mouse in my left and and use the arrow keys instead of WASD. my Razer Naga Left handed edition is a godsend.