Implementing a design into an FPGA on a PCB is done in the Devices view. Here the FPGA project, in combination with a configuration, is targeted to a board. An example is shown in Figure 1.
Figure 1. The one FPGA project (RateController), targeted to different FPGAs, on two different boards.
For the Configuration to be valid, it must include:
When the Live option is enabled the system searches for a physical device that matches the device specified in the project configuration and assigns that project to that FPGA/board. If there are no valid configurations available in the project, you will not be able to select an FPGA project/configuration in the drop-down list.
Since the FPGA design is target-independent, the synchronization process actually happens between the constraint file and the PCB project, rather than the actual design captured in the FPGA project source files.