I had the same problem at first. Copy the entire contents of your UI\Default folder to a working folder. Tell UIBuilder to open WorkingFolder\eq2ui.xml. Select MainHUD from the tabs in the preview window and you should be able to see what you're working on, assuming it isn't set visible=false (the eye icon above the attributes box) and it's high enough in the layer order (the arrow keys above the container list.) Hope this helps.
Edit: Oh yeah. Once you're done making edits and save, copy only the modified files into your mods folder. Things can get ugly if you copy some of those files into a playable mods directory.
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