I have read the application notes AN84868 -- Configuring an FPGA Over USB Using Cypress EZ-USB FX3. I also referred to the Xilinx Spartan-6 FPGA Configuration User Guide. Over the FPGA, there are mode pins M[1:0] used to select certain mode to configure FPGA. For example, M[1:0] = 11 indicates slave serial mode. However, in the application notes AN84868, there is not a discussion about M[1:0]. How should I set M[1:0], follow the Xilinx Configuration guide or just ignore?
You can either select the M0 and M1 pins either both ON, or both OFF. It does not matter in this application. So basically you can ignore these switches.