Before wiring everything on the PCB, let's check the Spartan-6 configuration sequence from microcontroller.
On power-on, both boards (microcontroller and FPGA) will get power supply, but only the microcontroller chip will start because the power supply rail of the FPGA is controlled by a relay which will be open by default. When the microcontroller board is ready, it can switch the relay and supply the FPGA.
By releasing the reset signal, the FPGA begins its start-up sequence, and sample the mode pins (M[0:1]).
During the configuration sequence, the bitstream is sent word-by-word in parallel (D[0:15] = 16-bit).
About the SelectMap clock
There is a whole section of the Spartan-6 Configuration User Guide ([UG380]) dedicated to the Board Layout for Configuration Clock (CCLK). Serial connection of several FPGA has to match specific requirements. See [UG380] v2.5, p.54.
|[UG380]||(1, 2) Spartan-6 FPGA Configuration user guide http://www.xilinx.com/support/documentation/user_guides/ug380.pdf|