1) To Modify the Navigation Items: Open the navigation menu from the Project explorer, you can edit your navigation items, add/delete/edit whatever you want
2) To change the logo in the Navigation Bar/Header: Open the app in Studio from the Developer Portal and Open the Theme Customizer by clicking on the brush icon on the left
Upload your custom logo and click Save.
Go back to Mendix Studio Pro and, under the Version Control tab, click Update.
3) To Create a completely custom Layout of the Navigation Bar/Header : In the Project Explorer, go to App Store Modules > Atlas_UI_Resources > _Layouts.
Right-click the Responsive folder and select Add other > Layout.
Name the new layout Atlas_Custom_Name whatever name you want to give
In the Properties pane, set the Master layout to Atlas_TopBar. Select the Scroll Container and in the Properties pane, set Scroll behavior to Full widget.
You can make the necessary changes to the layout here, according to your requirements
Open the home page. Set the new Atlas_Custom_Name layout as the navigation layout for the home page
you can create your own layout by right clicking your module then add others then select layout and create layout accordingly your requirement