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The XDS100v2.ept is a template for FTDI's MProg utility for programming the EEPROM connected to the FT2232H chip. They can be programmed separately. Both can be programmed after assembly. Program the EEPROM first using MProg. Then you can program the CPLD via it's JTAG connection through the FTDI chip using the utility posted on the Wiki.
MProg is only programming the EEPROM that's connected to the FTDI chip to set the USB enumeration info such as device name, VID, and PID.
In the FAQ section of XDS100 Wiki there's a subject on updating your CPLD: http://processors.wiki.ti.com/index.php/XDS100#Q:_How_can_I_update_the_CPLD_on_my_XDS100v2.3F which directs you to a utility by Spectrum Digital for programming the CPLD over the USB connection: http://support.spectrumdigital.com/ccs40/xds100v2/.