I use PDFill PDF Tools free software quite a lot when indexing from PDF files (I don’t usually work from paper print-outs). I use the split function when the preliminary pages are numbered separately from the body of the text, and then causes the page number displayed at the top to not match the actual number of the page.
More detail: http://www.pdfill.com/pdf_tools_free.html
PDFill PDF Tools (Free)
