One problem that can arise from this scenario is that a traditional print document's cover page and preface material will not carry traditional page numbers.
Take a look at any book on your bookshelf. The preface material and table of contents will likely have a separate numbering system–often times in lower case roman numerals. The "regular" Arabic numbering will begin when the book's subject matter begins.
Converting this same document to PDF automatically throws a monkey wrench into the works. The first page of any PDF file will initially be page 1. Perform a Go To Page command and you'll land on a different page than if you opened the print version.
How can you make the PDF version match the traditional print page numbers of its printed counterpart? Read on…
In this example, I have selected pages 1-4 in the Pages Palette, and then clicked on the palette's Options button (the gears).
I then selected the Number Pages command. I dialed in new settings for those selected pages by choosing Begin New Section and specifying Lower Case Alphas from the check list.

The end result is a document with pages i – iv as preface material and the main content beginning on the document's fifth page, but carrying the page number 1. Now the PDF file matches the print version's page numbers exactly.

These small details make your PDF files stand out from the rest. To learn more… MUCH more, enroll in an Acrobat 9 class. Click here for more details.