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Adding/Editing paragraph styles works for me. In fact, the ePub Template is just like any other Template for the Web Exporter. You can simply edit/add Styles in the EPUB.plist file.
Please bear in mind that you need to restart Ulysses in order to update the Template settings.
That's because ePub consists of XHTML and CSS files, internally.
Paragraph Styles (and also Inline Styles, Markers) are (usually) exported to a certain tag, for example Emphasis is exported to <em></em>. Or paragraphs with a Heading are exported to <h1></h1>. You would need to change the CSS file, for the ePub export this file is in css/book.css. Here you can adjust the look of each tag.
However, please be aware that iBooks ignores pretty much every style change since it wants ePub books to look as uniform and nice as possible. You can use Adobe Digital Editions to take a look at ePub books on your Mac.