By default Elementor should automatically replace the theme elements. The only part that may be left to change is the GP header container which you can hide by reducing the padding to 0 in the Customiser.
GP 1.7 is about to be released and the new Elements module will allow you also to disable the header and footer and replace them with your own content including Elementor shortcodes.
If you want we are more than happy to help you achieve your header footer designs with GP.