If you wish to use your yubikey with web services it will work out of the box. If you wish to use it as a smart card you will need(?) to compile yubico's software. I did all of that and set up my yubikey without much problem (even using my own OTP server), though there were some hiccups with their build system... they managed to screw up cmake in some creative ways.
All of the instructions should work fine once you get the software up. It would just be setting up gnome, etc, to use it. Probably no way to do something unfortunate to the hardware.
