For any other newbies to the Atahualpa theme, I thought I file this follow-up. I found the place to do this. The big problem was not being familiar enough with the theme. It suddenly occurred to me that the theme options was basically the same as Wordpress' .custom file. So for anyone looking for this answer, you put the code for the images, as well as a lot of other codes, under the "Add HTML/CSS Inserts" main tab in the "CSS Inserts" box. After realizing this, it all made sense.
PS: When writing the route for the images, Atahualpa requires an absolute route rather than a short code; example: "background: url(/wp-content/themes/atahualpa346/images/myimage.gif)". If that doesn't work, put your site name in front of "/wp-content". But if you want to not worry with replacing the images if you change themes, you can just place a folder in your "wp-content" folder and use the route to it. That way the images will always be available for any theme you use.