Bryan, I get an error when I try to search for Atahualpa via the "Add-theme" area of wordpress. But that may just be me. However, I have successfully downloaded the theme as a zip file from the download page http://wordpress.bytesforall.com/?p=92
& then used the built-in theme uploader to install & activate the new theme.
You want to make sure that you are creating a NEW theme folder (don't try to overwrite your old one!) so if your current theme folder is just called "Atahualpa" you want a new folder called something like "Atahualpa 3.5.1" installing it this way should do that for you anyway.
You'll need to copy/upload any header images & favicon to the new folder. Then you can preview the "new" Atahualpa theme and make sure everything looks correct. Activate it, check it again page by page if possible to make sure everything is working correctly for you...
If it's not, then you can always switch back to your original Atahualpa theme.