Am I missing something? No sidebars are displaying on any area of site using this template. Can someone help, please?

No sidebars at all or are they empty? If they are empty you may need to add widgets to the sidebars. If they're totally gone see if they're unchecked at Atahualpa Theme Options -> Sidebars -> LEFT sidebar: Display on: / RIGHT sidebar: Display on:

a couple of weeks ago I used the option to not display sidebars in certain pages. However, now when I have tried to add pages to that list (I changed permalinks to not display the page numbers) the sidebars show up and there doesn't seem to be a way to affect the change on any page.

pineknotfarmandlab.com

are you saying that when you add a page number to ATO->Style & configure SIDEBARS->LEFT sidebar: Don't display on Pages: it doesn't stay there?