PIN Assignment for Embedded Evaluation Kit (NEEK), Cyclone III

Well, usually you'd write a top level module that declares the I/O signals you need in your design, compile it, open the Pin Assignment editor and start assigning signals to pins.

To know which pins to assign your signals to and which I/O standard to use, you need to read the board's schematics and/or documentation.

In this case, it's the board's Reference Manual.

For example, the Reference Manual say's that there's a 50 MHz clock signal connected to FPGA pins B9 and V9, using 2.5V I/O.

So, if I want to use a 50 MHz clock signal named "clk" in my design, I need to assign "clk" to pin B9 or V9 and select the 2.5V I/O standard, using the Pin Assignment editor.

However, in that board's documentation, there's an example project where all the signals that are connected to the FPGA have already been declared and assigned.

You'll find it in examples/cycloneIII_3c25_start_golden_top