using altera FPL and choosing the configuration file in real time

You need to provision the bottom boot address into the CPLD before you initiate the FPGA boot. Assuming you have some connections from the cpu to the CPLD then you can use these to indicate which boot image to use. Alternatively, you may have jumpers connected to the CPLD with which you can specify the image you wish to boot the FPGA with. Either way, you will have to write some code for the CPLD to interpret the cpu signals or jumpers and provision one of four boot addresses.