Comment: Using navigation sections, boxes and sample boxes

" box is in the right hand menu "

Actually, navigation boxes (that appear on all pages) and extra boxes (that appear only at the home page) are just plain ordinary articles, but anchored to special sections.

Therefore:

 To add a box, browse the adequate section, and hit the link to create a new page. You will have to publish the page to make it actually appear at the right place.

 To change the content of a box, go to the adequate section, and edit the related page.

 To replace a box by another one while preserving the old one, you can create a new box, publish it, and un-publish the old one.