That's not how MergeDocx is intended to be used.
Do you want the same header and footer on each page?
Is the content source all in a single section?
If yes to both questions, you just have a sectPr element at the end of the content which specifies the header and footer parts.
Copying in the header and footer parts are simple (using plain vanilla docx4j), unless they refer to other parts (ie contain images, hyperlinks or the like). If they refer to other parts, you'll need to copy those in as well.
Also, if the header or footer uses styles or numbering, those definitions will need to be present.
At some point, it starts to get complicated, and then some of the machinery in MergeDocx is helpful...