hi chris,

  you can either submit it through the dataconnection to a webservice or
either through custom script(avilable somewhere on the msdn), once you recive
the xml use sharepoint object model to add a file to the form library
(avilable in the wss sdk).

note: when u submit the document to a ebservice infopath adds a parent
element to the Xmldocument

look at the following code i created a webservice function that receives an
xml document and then i manipulate it.

public void HelloWorld(XmlDocument xx)
        {
                try
    try
    {
                kk= new XmlDocument();
                kk=xx;
                oxml=kk.OuterXml;
                XmlNamespaceManager nm=new XmlNamespaceManager(kk.NameTable);
                nm.AddNamespace("my","http://schemas.microsoft.com/office/infopath/2003/myXSD/2005-03-20T13:32:11");
                nm.PushScope();
                string ContractName=kk.SelectSingleNode("//my:ContractName",nm).InnerText;
                string QueryType=kk.SelectSingleNode("//my:QueryName",nm).InnerText;
                string
QueryDescription=kk.SelectSingleNode("//my:QuertDetails",nm).InnerText;           
                string
QuerySubmittedBy=kk.SelectSingleNode("//my:QuerySubmittedBy",nm).InnerText;
                string Phoneno=kk.SelectSingleNode("//my:Phoneno",nm).InnerText;
                string EmailID=kk.SelectSingleNode("//my:EmailID",nm)

after this use the sharepoint object model to add the file to the form
library.

cheers
Bart