Hi Tom,
We have to Connect the resistor to a supply that provides an acceptable input signal for the FPGA device.
VCCPGM must be high enough to meet the VIH specification of the I/O on the device and the external host.
Most important point is that the operating voltage(VCCPGM ) for the configuration input pin is independent of the I/O banks power supply, VCCIO, during configuration. Therefore, Cyclone V devices do not require configuration voltage constraints on VCCIO.
Let me know if this has helped resolve the issue you are facing or if you need any further assistance.
Regards
Anand