Could some one explain some thing in this schematic please :)

ahhh yes sorry when u said Morphic II it did not click, now i remember that is the FTDI FPGA module :) i did have a good read about this when i was first researching this project and it does do exactly what i want!!! but it was missing the FPGA config eeprom and i was not 100% sure how i would add this into its design/ if it was even possible to program a FPGA config eeprom using JTAG.

looking at FPGA schematics none of the JTAG pins seam to go any where near the EPCS4 but im guessing you just connect it to the FPGA as normal and when you use JTAG it programs the FPGA and then the FPGA also writes the data to the EPCS4?