It sounds, from the limited info available, that the easiest way to do this would be to pick the chapter that's closest to what you want the end product to be and SaveAs the file to a new location to create your template. Then modify that file as needed -- there are a number of tools within FM that allow you to copy in portions of other files that will enhance your chapter template.
When you have the template in shape, you can apply it -- or portions of it -- to all files in your book with one command, and then clean up the outlying elements.
Art