A namespace allows Word (and you) to identify exactly which xml file you are looking at. Your sample document has two documents with no namespace - so the second one is shown as '(no namespace)(2)'. If the first one was deleted then it would likely appear as a different entry and possibly break all your linked CCs.
If you create the xml file and put it into the template, any new docs created from that template would already contain the xml file.
I can give you code to work on your provided sample doc but you have a bunch of unnamed CCs and so there would be a lot of missing pieces until that is resolved. A better solution to make you self-sufficient would be to point you at Greg Maxey's site where he has a very slick tool which is very useful for this type of task.
See
Content Control Tools