The approach I've used in the past is to create the PDF templates as fillable PDF Form, generate an XFDF (XML Forms Data Format), and use a tool that can merge XFDF into the PDF Template Form, and flatten the filled data into PDF (flattening a PDF form replaces the form fields with the filled data).
You can use Acrobat to create the template form.
XFDF is just XML, so it's fairly easy to generate with any tools that can generate XML.
One of the tools I've used for merging and flattening the form is pdftk.