How can I configure the FTDI FT220x for multiple SPI slaves?
Not sure I fully understand your question but the bus on the FT220 is activated from your master (i.e. microcontroller) via the CS (chip select) pin.

You shouldn't have to reconfigure anything to communicate with another shave.

Edit
Right, I see the issue now. It looks like (as you say) the option to set this isn't in FT prog. Sorry but I haven't used one of these devices before so not sure. I think you may have to look up where the setting is in the EEPROM and try changing it manually (which I think you can do in FT prog).

Have you ensured you've got the most upto date version and also that the correct device is selected?