Updating an existing document in your Saved Templates section is very easy. Simply open up the document in Microsoft Word, make your desired changes, and save the document within Microsoft Word ("file" -> "save"). Then, follow these instructions:
Go to Saved Templates in the menu of Advanced Document Automation.
Click the Upload New Template button.
Save the document to your Saved Templates once again via the Saved Templates page within the add-in (click the "Add current" button). The add-in will give you the option to overwrite the existing version of the document in your Saved Templates or to keep the existing document and add the new one as a separate document.