The new WP 4.7 has a custom css option where you can add this or just add it to your theme’s style.css file. Simply give your upper section a class name and remove the negative margin (set it back to default). In this example I’ll use the class name upper-section.
Save and then view the page and choose customizer from the wp-admin bar. From there you can simply add:
body:not(.elementor-editor-active) .upper-section {
margin-top: -5% !important;
}
The breakdown is that Elementor places it’s editor controls right inside the actual content we are editing so sometimes the look we are going for (styling) breaks that usability. We know that every page has a “body” tag and it only has a class of “elementor-editor-active” when viewing the page in the Elementor editor. This rule basically says to only apply this rule when the “body” tag does NOT have that class, thus don’t apply this style when Editing in Elementor.