There are several ways to do this, each has its own pros and cons.
Access XML documents externally. For this you need to persist the document as a file. Pass along DOM Document objects. This is very useful if you have already parsed the document. Use SOAP messaging between the applications and simply embed the XML document in the message. This has the highest degree of overhead, but can work very well with non-Java applications too.
Since I don't quite know the exact requirements, I am not in a position to say which one of these best suits you.
Cheers.