The configuration part is a Micron S25L128SAGMFI011. Their data sheet just talks about voltage levels, not whether the voltage needs to be the separate programming voltage for the FPGA. What does the FPGA expect regarding those EPCQ data inputs?? I remember that the Stratix III parts had reference designs that showed that the configuration part needed to use the same voltage source as the programming pins. I am unable to find anything similar for the Cyclone V parts.
You may find the information such as configuration pin's voltage and connection in our pin connection guidelines user guide.
For cyclone V, it is as attached:
Sorry the message continues here:
The voltage for every pin including the bank and powerail for main power pin can be found from page 40.
For cyclone V configuration pin, you may take a look at our handbook: