Xae and Xinclude question

Hello,
I am evaluating the xae, emacs, docbook tool chain for use in a
multi-author environment with a good size mature set of documentation.
One of our first requirements is the ability to modularize the
documents. I tried using internal subset entities but immediately ran
into the problem of trying to maintain documents without a doctype
declaration. This limitation prompted me to look for an alternative,
which I see with Xinclude. I found some info on this in Bob Stayton's
chapter on Modular DobBook
(http://www.sagehill.net/docbookxsl/ModularDoc.html).

I'm at the part about "Using Xerces to resolve Xincludes", where he says
to "add a couple of options to your java command." Here is the command
with the suggested options:

java -cp "/xml/saxon653/saxon.jar:/xml/xerces-2_6_2/xercesImpl.jar" \
    -Djavax.xml.parsers.DocumentBuilderFactory=\
       org.apache.xerces.jaxp.DocumentBuilderFactoryImpl \
    -Djavax.xml.parsers.SAXParserFactory=\
       org.apache.xerces.jaxp.SAXParserFactoryImpl \
    -Dorg.apache.xerces.xni.parser.XMLParserConfiguration=\
       org.apache.xerces.parsers.XIncludeParserConfiguration \
    com.icl.saxon.StyleSheet \
    -o bookfile.html \
    bookfile.xml \
    ../docbook-xsl-1.68.1/html/docbook.xsl

I cannot figure out where xae makes the java call in order to add these
options, if that's even possible. Can someone enlighten me? Is there
another way to resolve Xincludes with xae? Is there a better way to
achieve modular documents? Is there a better forum for this question?
Thanks in advance.