Your Spartan chip should now be at firmware version 0x6. Do not cycle the power at this point.
Use either AMC13Tool.exe in the C++ software or p_flash.py in the Python software to update the flash for your Spartan and Virtex chips. You should program all 4 flash images (AMC13T2Header, AMC13T2Golden, AMC13T2Vxxxxx.mcs and AMC13T2Vxxxxx.mcs). After this last step is complete you should cycle the power and check that your versions are now the latest ones.
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Program FLASH using iMPACT
Download the desired MCS file to your computer (in a known, accessible location)
Connect your JTAG cable to the bottom-most of the two 10-pin, rectangular, male sockets on the front panel of your AMC13. Note that "pin 1" is in the upper left-hand corner of the connector