Open atahualpa.pot in POEdit (free software that you need to install). In POEdit you'll have a blank text area for each piece of text in the Atahualpa theme that POEdit found. Put your translation into these blank text areas and save the file as i.e. de_DE.po for a German translation.
POEdit will automatically create a de_DE.mo file while you save the de_DE.po file. The .mo version is the file that will be used by Wordpress. To edit your existing de_DE.po file again, edit, save as de_DE.po again. This will create a new de_DE.mo file and overwrite the old one. You can also edit an existing .po file in a text editor. But to create a new .mo file you'd need to open and save it in POEdit.
See also http://urbangiraffe.com/articles/tra...s-and-plugins/