The most common problem with CP art application is to cut the holes in the CP before using the CPO as a cutting template.
If you set the CPO on the CP, make some small holes through the button / joystick centers on the CP and then cut, you will find your CPO will line up very well.
Other than that... I don't hear to many problems... Other than someone using the wrong materials, or getting bubbles, etc. With something from mamemarquees.com, you've started off on the right foot.