Using dedicated WebService Functions

There are two general approaches to updating an existing document's XML:

Retrieving, modifying and saving the full XML
Using more specific API calls

Updating the full XML

While definitely the most powerful of the two, it also might require more work to go through the documentation. But if you know what you're doing, it's really quite straightforward:

Use ?Webservice Functions - ResourceItemGetXML to retrieve the document's XML (resourceName = "Documents", itemID = the ID of the document you want to manipulate)
Modify the retrieved XML using the tools in your development environment (eg: the "XmlDocument" object in .NET)
Save the XML back to the document using ?Webservice Functions - ResourceItemSave

Dedicated functions

But depending on what you're trying to accomplish, there might be even easier ways. Various commonly used operations have more specific webservice functions, which accept subsets of the document XML, or even simplified versions of subsets. Examples are:

Previews or PDF not updating?

See ?General XML Concepts and/or ?Updating Variable Values and Definitions for more info on the XML validation (you'll probably need to set "savedInEditor" to "false" on the document's root node)