If you check the option "use dedicated active serial interface", you don't need to connect the port to AS pins, software will connect them automatically, and you will not see the port on the SOPC symbol.
If you don't check any option when you add epcs_controller, you need to assign the ports manually. The interface could be user I/Os or dedicated pins.
When the option is not checked and the interface uses the dedicated AS pins, you need to set the AS pins as user I/O in dual-purpose pins settings and assign the ports to the dedicated pins location to make them connected.