Although this video shows NB3000 users how to boot from the SPI flash devices (either on the NB3000 or inside the FPGA), the methods presented are useful for full custom board FPGA designs as well.
Learn how to load the FPGA configuration for Xilinx and Altera devices, and then continue on to boot the embedded code for the soft processor core from the same flash memory into SRAM using the SPI Bootloader IP Core.