No, the software doesn't allow to have page numbers printed on documents. I've checked the documentation pages and user guide available and it's nowhere mentioned about page numbering. For this procedure, you will need an application that is dedicated to edit PDF files or the format produced by eCopy Desktop.
Once you get the format, access the database of Software Informer to download applications relevant for the operation above: http://software.informer.com/search/pdf+editors