There are two methods available to apply the Tandem flow to a user design. The first method is to use the example design that comes with the core. The second method is to import the PCIe IP into an existing design and change the hierarchy of the design if required.
Regardless of which method you use, the PCIe example design should be created to get the example clocking structure, timing constraints, and physical block (Pblock) constraints needed for the Tandem solution.