I\'m writing the xsd and the code to validate, so I have great control here.
I would like to have an upload facility that adds stuff to my application based on an xm
Take a look at NVDL (Namespace-based Validation Dispatching Language) - http://www.nvdl.org/
It is designed to do what you want to do (validate parts of an XML document that have their own namespaces and schemas).
There is a tutorial here - http://www.dpawson.co.uk/nvdl/ - and a Java implementation here - http://jnvdl.sourceforge.net/
Hope that helps! Kevin