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The font settings for the Preview and Standard Mode are for display in Ulysses only. Thus, if you change the font for the Standard Mode, this will update the font in the Editor.
Ulysses is a semantic text editor, which means you give the text a meaning using Styles and Markers. During export, you assign a formatting (e.g., a font) to those Styles and Markers. Thus, during export, you could assign a heading a different font than the main text, or exclude commented out text from the export. To do so, click on the name of the style action in the column "Style" of an exporter and select "Edit…". If you want to change the formatting of the main text, click on the style action for the Paragraph Style "Main text" and select the menu item "Edit…". In the sheet, you can now do all necessary adjustments. For instance, you can set the font to "Bookman PS". Hit the "Save" button and then export documents.
I don't have "Bookman PS" installed on my system, but setting the font to "Bookman Old Style" worked just fine.