How to assign GPIO to pins I have assigned on DEO nano

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Is it the one talking about the requirements for 2.5/3.0/3.3V banks?

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Yes, that's the one. It's unfortunate there's a warning for which the only option is to suppress it. In this case, most of those signals are already wired up on the DE0-Nano to other components (e.g. SDRAM, buttons, LEDs, etc.) so I assume TerasIC adhered to an 447 (http://www.altera.com/literature/an/an447.pdf) when they designed this board.

Of course, much of Altera's library code has plenty of warnings so warning-free code is practically unattainable. Still, I don't want something important to get lost in a sea of innocuous warnings so I'll suppress this one.