How can I apply a Header or Footer?

Yes, there are a couple of ways you can create a header or a footer in PDFpen/Pro. In the latest version, choose Edit > Headers, Footers, Page Numbers > Insert.

You can also create a header or footer via AppleScript. For this method, choose the graphic you want to use. Drag the graphic onto the first page and position it. Then, choose "Imprint all Pages as First" from the Script menu. The header or footer should apply throughout the document. If you do not have a graphic, you can create a text box with the Text tool. Type your text in the box. Then, go to the Script menu and select "Imprint all Pages as First."