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If you export your documents via the PDF export, all documents are paginated according to the settings in the PDF exporter (you can find them in the section "Page Setup"). You can also insert a page break after each chapter by setting the export mode to "All in one file" and dragging a "Newpage" token into the text field for "Insert between documents" (this should already be the default setting).
You can find more information about the PDF exporter in the Ulysses online help and our screencast on exporting.