Arria II GX Development Boards Unused i/os

the PCG is good if you're designing a board, but if you're using a devkit i'm not sure its all that helpful.

setting unused I/O to input with weak pullup shouldn't break anything, but it might set (unused) peripherals into unknown modes or other unexpected behavior. then again if you aren't using that particular feature you probably don't care what mode its in.

you could take a look at the some of the included example designs to see what they have done with unused pins.