HSMC interface IO in SOPC Builder

You need to add a PIO to your SOPC hardware project first, then update the top level design file to connect those to external pins, and then use the assignment editor to set the exact pin used for each signal. I would recommend to look at the board schematic rather than the documentation to find out which FPGA pin is connected to which pin on the HSMC connector. Altera's kit documentations are known to have a few mistakes in them.