If u are into functional verification.. no need to look at FPGA architecture , I guess. If u r debugging a design in FPGA , may be you can start with reading the data sheet of the FPGA and FPGA board you are using....Find which all peripherals are available in the board and check out the interfaces to the peripherals...
One of the trickiest parts of this architecture are the ROCKEIOs .. so as suggested read the app notes but try to do a little project envolving this peripheral to get closer and hands on