Do you know sql and managing tables/databases? You are attempting to do basically the same thing here without a database. In that case, I would add an id attribute to your packages.
Also look into using ajax (jQuery can do it easily and well) to save your xml after every necessary change. It sounds like this is a pretty complicated script you are writing here; write out/plan everything you need the script to accomplish and how you would go about doing it. Then knock things out one at a time.
And you could give each li an attribute and have jquery read/change that value.