Reading is addictive. It is a common perception that you need to read essentially for your conceptual framework and review chapter. There is probably no bigger myth than this. There is no chapter that can be written without adequate reading. You will be reading for data analysis, tool development, and for everything else that is between the cover pages of the thesis. You will probably be reading on writing, and maybe even on reading itself!
However, reading in itself, without being supplemented with writing can be disastrous. For one, reading is not a phase. You cannot begin by preparing your conceptual framework and review chapter and then close it for the rest of a minimum of three to four years you would spend in completing your work. You review will become dated and your research will lose on contemporaneity. If you do it in the end, the rest of your work will be devoid of contextualisation. Review, in other words, is an iterative process that continually evolves throughout your research journey. Now the important bit is to recognise that you cannot possibly remember everything that you have read over four years and then compress it into a chapter at the end of the research. Thus, the need to write what you read.
If you end up with a hundred references in your PhD thesis, you are likely to have read at least four hundred. Who can remember why you read something a year back and decided to put it in your folder marked as important? Merely underlining or highlighting what you feel is significant when you are first reading only tells you that when you read it again, you are likely to pay attention to what has been highlighted. To understand that one sentence which is highlighted, you may end up reading half the research paper/article/chapter again. This means that your initial effort in reading something has been reduced to zero.
Besides research work, if you are an avid and curious reader, you must remember that you are not likely to read the same piece of writing more than once. Unless it has literary value or it serves a specific purpose for which you are reading it again, you are very likely to read it once and toss it aside till the time you realise that you have forgotten why you downloaded/ photocopied it in the first place. It is for chiefly this reason that I am suggesting making annotations.
Writing annotations is a little bit like making notes and then supplementing it with what is likely to be relevant to your research. You may want to make a separate notebook/ word file/ one note file for writing anecdotes. What I find also useful is to use index cards or A5 size sheets that can be stapled at the end of a reading or chapter. An annotation must contain research reference of the article, a summary of key points of the article, and most importantly, what you found relevant in the article/ paper/ chapter for your own research. So you may want to note down the sampling technique used in a particular research and then use the same in your own. But if this reference is not readily available, you may end up sifting through thousands of papers to find that one line that is actually relevant for you.
You may want to categorise index cards later according to the area that reading is covering. Thus you may keep index cards by concepts covered, relevance for methodology etc. While it is not a hard and fast rule, annotations should generally summarise the article in the researcher’s own words. This would help you to capture the essence of the reading as well as save time that you may end up spending only in copying. It would also help if you classify your reading and annotation cards/ register according to some indexing system you might evolve. This would help to keep your personal library also organised.