I cut the centers out leaving just a little of the plastic to hold it together. Added some registrations marks to help with lining it up on the quilt.
Here is one of the designs marked on a non-trapunto area using the Clover white marking pen that can be erased with water. The pen is a ball point version so you can get a pretty fine line using it. It is a little tricky in that you can't see the marks right away but they do show up after a minute or so. It is easy to keep marking until they show up but that isn't necessary - patience will to the trick.