Hi Allan,
Here's a screenshot of the front page of a letter using the Photo Letter template, and showing the document margin and header/footer settings. Show layout has been selected to show the 'boundary lines on that page.
Notice that there are no entries in the header or footer boxes. Anything placed in these boxes s treated and a 'running header' and displayed on every page of the document.
Top margin for this page is controlled by the height of the picture frame container holding the photo. If your letterhead logo is mostly text, that frame could be replaced with a text box, set to Stay on Page, and to wrap (text) Above and Below.
The picture frame or text box are not in a header box, and are not placed in the Section Master, so they will not repeat on succeeding pages added to this document.
This template produces a word processing document, so, as body text is added, Pages will generate new pages to accommodate that text as needed.
Your template may be similar, and can likely be set to exhibit the same behaviour.
Regards,
Barry