How to access the selectmap pins (both hardware and software) in Virtex 5 development board?
The programming pins are hard wired to the flash chips (SystemACE and Platform Flash: U2, U4, U5). This is documented in the ML50x Schematic file.

You could use the JTAG interface (J1) like a regular programmer does. If so, you need the Raspberry Pi to talk the JTAG protocol.

An alternative solution is to upload a flash programmer design to the FPGA that interfaces the flash chip to a common link like UART. This is used by iMPACT to upload bit files into the flash for permanent storage. First it uploads a design into the FPGA and then it uses this design to move the data from JTAG through the FPGA to the flash.