I just had a quick look at the Parallella schematic. It is 17 pages with rather a lot of connections so I can't do a full analysis in a few minutes. (I would also need to work through the datasheet)
You must check which voltage your I/O pin is operating at. If it is 3V3 you can use the schematic as-is. If it is a different voltage you have to replace the 3V3
with whatever the I/O voltage is. For the rest the principle is OK: Pull the port low with a resistor and use a push button to the selected voltage to make it active high.
If you don't know which voltage to use set the pin in output mode and output a 'high' Then measure which voltage appears.
Note that in general it is safer way to use a resistor (e.g. 50KOhm) to tie the pin to the I/O voltage. Then use a push button to pull the pin low. If you make a mistake, the pin is more likely to survive as the resistor limits the current.