in my opinion,you should define the pins of FPGA first.
Then you should configure your FPGA
There are 3 classical ways to configure your FPGA:
1)You use a cable from your PC to the FPGA, and run a software on your PC.
2)You use a microcontroller on your board, with an adequate firmware.
3)You use a special PROM on your board, connected to the FPGA, that configures it automatically at power-up (FPGA vendors have such special PROMs in their catalogs.
Last,you can verificaton the function which you intended on board.
Regards