For the Header and Footer, you need to set up and position all of your elements (the menu, images, text, etc.) separately within EACH viewport.

You cannot just set up the desktop view and automatically expect all the Header and Footer elements to automatically locate themselves properly.

Dennis, if you delete an object in any resolution it is deleted in all resolutions (there is a warning message), this also applies to font sizes. However, if you resize or reposition an object this affects ony the current resolution. Keep in mind the title object will allow you to scale content by simply resizing the object.

If you can not use an existing object at or below a specific resolution you can hide it for "this and lesser resolutions"

If you now add an object (eg an alternative menu object) it will only display at that and lesser resolutions.

Perhaps a screen shot of template content at desktop and another at the lesser resolution with a problem might help us help you?