I can't seem to change the default font that other styles (such as headings and footnotes) are based off of for new documents.
Here are the steps I'm taking:
1. Format -> Style
2. Modify Normal
3. Font -> Select preferred font and click Default, then click OK
The fonts are then correct in the document I'm working on, but when I open a new document, the fonts for headings & footnotes don't reflect my preferences, and are instead the Atlantis font default. The font is correct when I'm typing regular body text.
(Apologies if this has been covered already, when searching the forum the search terms weren't permitted as they were noted as being too common)
Unable to change default font for headings and footnotes
Re: Unable to change default font for headings and footnotes
If I am following you correctly, the problem is that you do not understand Templates and Styles.
When you change the Normal font in the current file, the change is not supposed to affect other files. It affects only the current file.
If you want a change for subsequent new files, then you have to change the Normal template, or you have to create a new template that you can choose to use when you start a new file.
Try reading whatever the HELP file has to say about Templates. You can probably modify the Normal Template (I have never tried). What I do is to create new Templates and save them, and then I can choose the Template that I want to use. When you start a new file, you can select FILE > New > Select from Template. Explore the FILE menu and look at the various things there.
I have thought about writing an article to explain Styles and Templates in Atlantis. In fact, I started one a couple of months ago, because another forum member was totally lost. But honestly it is difficult to explain it all, because the intended readers usually have no foundational knowledge, and everything has to be explained in excruciating detail.
But, really, it would be helpful to you if you explored the subject of Styles and Templates. I assume that the HELP file has information about these.
When you change the Normal font in the current file, the change is not supposed to affect other files. It affects only the current file.
If you want a change for subsequent new files, then you have to change the Normal template, or you have to create a new template that you can choose to use when you start a new file.
Try reading whatever the HELP file has to say about Templates. You can probably modify the Normal Template (I have never tried). What I do is to create new Templates and save them, and then I can choose the Template that I want to use. When you start a new file, you can select FILE > New > Select from Template. Explore the FILE menu and look at the various things there.
I have thought about writing an article to explain Styles and Templates in Atlantis. In fact, I started one a couple of months ago, because another forum member was totally lost. But honestly it is difficult to explain it all, because the intended readers usually have no foundational knowledge, and everything has to be explained in excruciating detail.
But, really, it would be helpful to you if you explored the subject of Styles and Templates. I assume that the HELP file has information about these.
Re: Unable to change default font for headings and footnotes
I figured it out; I had to make the changes in Normal.RTF, and now the font styles appear to be updated for new files. What threw me off was the dialog box text when you are changing the default font in other documents:
Re: Unable to change default font for headings and footnotes
All right, great! 
Re: Unable to change default font for headings and footnotes
The "Default..." button in the "Font Format" dialog does not change styles. It applies the current font format to the entire text of the default document template. In other words, the current font format becomes the default font format for new documents. If you create a new document after clicking the "Default..." button, the new document will automatically have the font format loaded to the "Font Format" dialog at the time you clicked the "Default..." button.