Flagstone over existing slab with expansion joints in place

I bought the DVD and found it helpful, but I did not see this addressed in the video or on this site. I have a 650 sq ft project in mind. The slab is 8 years old and in good shape. It has expansion joints in it per code and is bordered on 3 sides by the foundation. I plan on leaving a half inch all the way around between the stone and the foundation and caulking there. How do I handle the flagstone where it crosses the existing expansion joints? Do I go back after the stone is in place and cut expansion joints in the stone to match the underlying expansion joints in the slab, or do I just let it be and fix the grout between the stones later if it cracks? Thanks