If you are already undertaking research then you ought to give serious consideration to having three notebooks. If you are thinking about undertaking research then we'd strongly encourage you to keep an account of your explorations. You will find, in time, it is all useful data for your research.
The idea of notebooks is not new. The use of three as we suggest is adapted from Bruno Latour1. It does not matter if you use physical notebooks or digital ones, or a mix. The most important thing is to use them. Notebooks are not a matter for assessment or evaluation, they are data! If you do them well, they will be a sound basis for all of the writing that you do along the way. They will help you with your writing.
The first notebook is where you write down everything you can about your journey.
The second notebook is for recording information about all the stuff you collect.
The third notebook is for your ad libitum writing. Think of this as the place where you make notes about all the good but distracting ideas I had while I was doing my research degree.
Apart from providing you with a rich and valuable account of your journey, you might consider using software that helps you find patterns of associations in your notes. Steven Johnson writes about this in his book, Where Good ideas Come From2. There is a presentation he gave to Authors@Google about his book on YouTube.