For your convenience, a reference video is available on the TrenzElectronic's Channel at YouTube.
For further reference, please read Xilinx XAPP974: Indirect Programming of SPI Serial Flash PROMs with Spartan-3A FPGAs and this discussion (in particular for TE0630 Spartan 6 module) on the Xilinx forum.

To indirect program SPI Flash using Xilinx iMPACT do following steps:

• Connect JTAG cable to corresponding module connector (see JTAG connector).
• Connect JTAG cable to host computer with installed Xilinx iMPACT software.
• Power-on module by external power supply source or by USB cable.
• Run Xilinx iMPACT.
• Select Boundary Scan mode.
• After initialization iMPACT window should look like

• Right click on FPGA image and select "Add SPI/BPI Flash..." from menu.

• Select mcs file to program.
• Select SPI Flash type corresponding to your module type and revision.

• Right click on Flash image and select "Program" from menu.

• Leave default programming properties and press "OK".

• Wait for operation to complete.
• After completion iMPACT window should show "Program Succeeded" sign.