You need to copy your FPGA configuration file (*.sof or *pof) into the intel flash. After power up your board, the FPGA internal circuitry should automatically load the configuration file (stored in flash) to the FPGA.
1. Check your FPGA configuration pins (MSEL0 to 3) are set correctly to get this behavior (refer to the datasheet). These pins should be configured to use AP configuration, check also nStatus, config_n and ce_n pins... (refer to the reference schematic from the eval board)
2. Before use the programmer to load the configuration file you probably need to convert your *.sof file into a *jic file (which mean "indirect JTAG") in order to load it into the flash and not directly into the FPGA (I need to do that with my serial flash data).
I hope it will help you,
Enjoy,
-Pierre