One way to think about annotation, as part of viva prep, is that it helps to emphasise parts of what is in your thesis. It’s not about last minute additions or pre-answering questions in the margin: annotating your thesis emphasises the good stuff that is already there, making it easier to find or easier to see.
You get to decide what you need. Make a list of what could help, then find a good way that works for you. Do a little work and you have an upgraded copy of your thesis for the viva.