Xilinx Spartan 3, SelectMap, Mode pins, Dynamic Reconfigurat

[video1]

I had one question about the Spartan 3 reconfiguration. I want to
configure the FPGA from a PROM at the startup, and that will be done
in master/slave serial mode so mode pins will have some corresponding
settings. Then I want to use the configured FPGA logic to reconfigure
itself. In this case since Spartan 3 does not have ICAP module, I will
need to use the selectMap interface (of course I will need to bring
out signals from the FPGA to connect to selectMap). My question is
what happenens to the mode and init pins duing this reconfiguration by
selectMap port. Do I just need to write the partial configuration bit
file using D, CS, Write pins? or I need to change the mode bits
settings too since I will be using the selectMap during
reconfiguration and I was using Master/Slave serial mode........or the
FPGA understands that it is partial reconfiguration and it does not
need any mode input setting..in that case, how it will differentiate
JTAG reconfiguration or selectMap reconfiguration.

Thank you
~Naveen