Writing notes and keeping information in a coherent format is a key part of the research process. Your initial literature search will reveal key concepts and themes, sometimes over and above those which you had anticipated in your search plan.
These themes serve as categories from which to explore your research plan - and this will take place over the next 3/4 years! Although you should aim to have a coherent literature review by the end of the first year, this is a working document and you will need to edit and revise it right up until submission.
Categories can be used to extract information ready to actively write your literature review. You need to come up with a robust and effective system to manage and retrieve all of this information, data and documents - it is worth considering some of the systems that you might be able to use - such as EndNote, Microsoft Word, Index Cards etc.