Highlighting words might not be so great, since it means that the part of the text that you are interested in will have worst contrast.
Writing in the margins, especially when he mentions writing between lines, means that you can underline and handwrite, and unless there is some special reason that the stylus won't work on the areas with text, you would also be able to cross.
That question was answered a day before Bogdan started this thread, which shows that he didn't bother to look at other threads.
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