After you've 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.
When you draw the form fields in Adobe Acrobat, you're drawing them on top of the template that you designed. There isn't 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.