When your document has no Header or Footer, you can rely on the Margins to be pretty straightforward - Top and Bottom margins are just blank space.
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But when adding Headers and Footers, especially in combination with Background Images, it adds a level of complexity that we have done our best to simplify for you. That's why we created the Header from Top and Footer from Bottom settings in Themes.

The best way to approach these is to think from "Back to Front" - start with the Background first - you may even have this already.  Consider where you want the Header Text and Footer Text, and how far from the Top and Bottom each needs to be, as well as the colour it needs to stand out from the colour of the Background at that spot.

Next, decide how far from the Top the main body of the document should begin and set the Top Margin accordingly.  If this is less than the Header from Top setting, it will be ignored.  It's there just to make sure that if you want to push the body down further because of the background, you can do so.

The same also applies in reverse for the Footer - decide how far down the body should go before it is forced onto the next page and set the Bottom Margin accordingly.  Then decide how far up the Footer Text should be from the bottom and set Footer from Bottom accordingly.

Note that in order for Word to apply the Margin settings for the Main Document (not the First Page Margins), it needs an explicit Page Break, which can be tricky in a dynamic document such as one produced by Automio.  If you find that your layout can't have a clearly defined break (such as in the pictured example where we aren't making a distinct Cover Page but rather just getting straight into the body), you may have to set the margins the same for Margins and First Page Margins.  This is because the Margins are applied only after the first Page Break.  This is not a shortcoming of Automio, but rather of generating dynamic Word documents in general.

For Cover Pages, this is easy, as they typically contain just a Title and sometimes some small amount of text.  Just follow those with a Page Break and the next page will have the Margins applied.