I figured out one way to handle this. After I have completed my document #1, then I can select a single node (the root) into a new DOM object. It works for my purpose.
oDOM2 = Createobject(MSXML2.DOMDocument)
<bunch of code and other things go here...>
oDOM1 = Createobject(MSXML2.DOMDocument)
oDOM1.Load("<SomeXML><MoreXML></MoreXML></SomeXML>")
oDOMTemp = oDOM1.selectSingleNode("//SomeXML")
oDOM2.appendChild(oDOMTemp)
Is there a better way?