The Modules Wrapper is a wrapper module (no pun intended) which serves basically one function: that is, to group modules together whether to be able to re order a large group of elements or to add a sidebar to its side.
This gets really helpful in the case you want to build a magazine style page with several modules containing posts collections, with a sidebar on their side, or to build a blog page with a sidebar.
To do that, just build your modules query by using the provided select box, and choose a sidebar, together with its position (left or right). You can create specific sidebars for this use by navigating to Theme Options >> Layout.
Please note: the modules availability and their specific settings depend on each theme, not all themes include the same modules with the same settings.