There a number of ways to do this, the simplest being to create a child thought with your notes under the relevant object (thought) in theBrain - you can then open the thought for the notes in a separate window and work on both thoughts in parallel. The drawbacks are that you don't really "annotate" the file (I use only .pdf files for such texts).
I have a similar need and, working with Windows PC and Android tablets have come up with a system that works for me as follows:
Sorry this has turned out to be such a long answer, but I hope it helps. If you are interested in how this system works with android tablets let me know.
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