Namespace containers are used to define a collection of XML namespaces, along with their preferred prefix values. Any number of structures can be associated with a given namespace container.
An XML namespace is simply a URI used to provide a context for the name of an XML element. This allows large documents to contain sets of elements defined separately without fear of name collision. In the XML document, the namespace is represented in each element using a namespace prefix, which is just a pointer to the full namespace URI. The namespace prefix itself has no significance. When comparing the names of elements, only the full namespace URI is used.
The namespace container simply provides a list of namespace URIs with their prefixes. When viewing a structure, the namespace prefixes are shown as part of the element name. If you prefer a different namespace prefix for a given namespace URI, you can just change the namespace prefix value in the namespace container. The namespace prefixes used in the structure editor are defined by the current values in the associated namespace container. If you change the prefix in the namespace container, this change is automatically shown in the elements shown in the structure editor.
If you are only using the XML Schema Instance namespace http://www.w3.org/2001/XMLSchema-instance, then you don't need to create a namespace container, you can just select the property on the XML representation.