The mark-up tool is sessional. This means that it will only save during the session, but not save when you close the book. When the mark-up tool is open you can't use the other eBook features or move pages. You will need to close the mark-up tool to do this.
Reopening the tool in the same session will bring up your annotations again. The tools provided in the mark-up tool are:
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Pencil
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Highlighter
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Eraser
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Shapes
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Post-it note
You can also change the opacity of the tools.