I guess you are talking about interface Node and interface Element in package org.w3c.dom. Have you looked at the API documentation for those interfaces?
Element is a subinterface of Node. An Element represents an element in an XML document, so something that begins with a start tag and ends with an end tag. An Element is a Node, but there are other things besides Element which are also Nodes. For example, attributes, comments etc. are also Nodes, but not Elements.
The org.w3c.dom API is not very well suited for editing XML documents - it is meant mainly for reading XML documents. If you want to edit XML documents, an API like
JDOM is much easier to use.