After you have converted a document to PDF, you define form fields that display the data from the XML input file. These form fields are placeholders for the data. The process of associating the XML data to the PDF template is the same as the process for the RTF template.
See Associating the XML Data to the Template Layout.
When you draw the form fields in Adobe Acrobat, you are drawing them on top of the template that you designed. There is not a relationship between the design elements on the template and the form fields. You therefore must place the fields exactly where you want the data to display on the template.