After being completely annoyed by SimpleXML earlier I decided it was time to look at DBXML again. This time I ran across a forum posting saying that DBXML 2.4.11 had a bug in it preventing updating. After upgrading to 2.4.13 I was able to update documents in a container. So I made some update to the project but realized that this was more of an out of control experiment than a real project. Already started redoing it, all the PHP is going to be new but I have managed to reuse most of the Javascript.
I also found this site DBXML With PHP, it is a small wiki for, as the name says, using DBXML with PHP. It has not been updated in a while (until today) but I will keep adding things as I progress on DBXML. Hopefully other will help out too, right now there are few resources for DBXML in PHP.