Use Xournal for highlighting and annotating.
Xournal is a great little tool. When you annotate a PDF (add comments, highlights etc.), you normally can save it into a ".pdf.xoj" file; this file does not contain the PDF (in fact, it is only gzipped XML) and is only used by Xournal to overlay your comments over the original PDF.
If, however, you wish to save the annotations and the original PDF to another PDF, Xournal can export an new PDF file consisting of the original file and your annotations.
That way, you can keep the original PDF without annotations, but you can also make your changes permanent if you wish.
To install xournal, type the following in a terminal:
sudo apt-get install xournal