Chances are very good that you have a bunch of PDFs scattered around your Mac’s hard drive right now, and you can use PDFpen with any of them.
But real Iron Chefs cook up their own PDFs:
If you’re a complete do-it-yourselfer, you can make a PDF entirely from scratch (see below).
If you prefer to work with prepared ingredients, you can make a PDF from almost any document your Mac can print. See Print to PDF.
If you like imported delicacies, you can Import from Scans and Graphic Files to make a new PDF, and even perform optical character recognition (OCR) on them.
If you like to work with leftovers, you can make a new PDF from the bits and pieces of other PDFs you have hanging around. Read Combine Existing PDFs.
Or, if you like ...