Usage of dual purpose pins

First of all go to project settings, Device section; select "Device and Pin Options", then the "Dual-purpose pins" tab.

Here you'll have to switch EPCS pins to "Use as a regular I/O" mode.

You can now assign to this pins any signal you want.

The only point not clear to me is why you want to use a 4-bit pio, as you have the nios epcs controller readily available.

Please note that you are usually supposed to use these dual-purpose signals to access EPCS itself after configuration (with Nios or whatever you implemented inside fpga). Although it's possible to use them for other purposes (ie. controlling other hardware devices connected in parallel to epcs), remind that you must take extreme care to avoid signal contention between the two paralleled devices.