Here's 2 pictures, compare to what you see when you use builder...
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You should see something like the 2nd picture. When editing with builder, mainly you'll be opening the eq2ui.xml file and it's all visible from there. Make your changes and save, and it will automatically create (or overwrite) the proper .xml file that it needs to. (ex: if you F with the experience window it will either create or write to eq2ui_mainhud_experience.xml on it's own)