Following the previous queries, the external SPI FLASH (W25D32) with the data written at location 0x000, should be connected to D10,D9,D8,C10 or E3,E4,F4,F5 ?

References to "flash2" are for the support of a second flash SPI chip to connect directly into a user project. This has no defined function other than that the housekeeping SPI can make a direct connection to these pins to program a flash IC using the same method as used for the on-board flash chip. However, it's up to the user project to define the actual flash interface. All other references to flash interface pins are for the flash chip on the evaluation board. So the short answer to your question is D10, D9, D8, C10.

Thank you this clears it up.