If you want to be able to access the quad SPI flash that is used to configure the image for the FPGA after the configuration is complete, you can instantiate the alt serial flash module that will allow you to access the FPGA pins connected to the SPI device. I use this block to allow my SPI flash config memory to be accessible via the JTAG chain, but it has capabilities beyond just this function.
All the details are here:
https://www.altera.com/literature/an/an370.pdf (
https://www.altera.com/literature/an/an370.pdf)
You want to look at the 'Share ASMI interface in your design' option description.