I have always had trouble organizing creative projects. When I'm working on a picture book, that is not so much of a problem. The text and plot line are short enough that I can memorize it all and keep it visually straight in my head. Reference material will usually all fit onto one table. But I've been working for a couple of years on a longer manuscript with a plot that is more complicated than the picture-book level. The process has turned into a kind of aimless wandering through a literary bog. The result has been mounds of papers, files, folders, notes, old envelopes, and reference materials. Yes, the mounds are all stacked in piles together on the shelves of one bookcase. But I have learned through sad experience that this does not qualify as "organized" or "useable" or even "findable". As a result, I've been going in circles---adding more and more to the mounds, but moving no closer to the completion of my manuscript.
Like many authors, I'm always collecting How-To-Write books. I recently came across this one. (It has a companion, The Marshall Plan For Novel Writing). Hope springs eternal in my breast; though no other How-To book had ever enabled me to make even a dent on my struggles, I snatched this one up as a possible thread out of the labyrinth in which I had become trapped. To my astonishment---and delight---I have found parts of it very helpful.
I am still working slowly; that probably will never change for me. But my manuscript is now contained---manageably---in one notebook. I FEEL that I am progressing with the project. (I don't yet dare assert that I AM progressing.) The Marshall Plan Workbook may not appeal to anyone but myself; we are all different in the ways in which we write. But then again, it might be just what you were looking for. So I pass this experience on, for whatever it's worth---and no, I am not being paid to do so!