Xilinx Spartan 3, SelectMap, Mode pins, Dynamic Reconfiguration

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

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