My practice over the past 40 years or so has been to identify an issue or subject I want to write on, but to confine my reading to a few major works (to ensure I am alert to the main issues) and to work directly on the text(s) to draft out what seems to me to be the main concerns and arguments. Only then, with a paper in first draft, do I go into intense study of as much of the main secondary literature as I can lay my hands on. This may explain why in most of my writings most of the argument with other scholars comes in the endnotes.
Since my preliminary draft will have identified most of the issues to be discussed, when I do the more extensive secondary reading the notes I take are of direct relevance to the issues identified.
This question comes too late for me. I developed my own style well before Dropbox, etc. was available. And in what I have been doing since these tools became available it wasn’t really necessary to change my practice.
I would press the value of the practice I have followed, since it allows the texts to throw up the questions and enables me to order the results of my reading in accord with the text and the issues/questions raised thereby. It would seem to me to be important that the texts being analyzed or discussed always have primacy and the secondary literature be treated as secondary.