Let me clarify my method. I will, at points, write my own insights in the margins of that Bible. However, here's my general practice. If I come across a writer who has a particularly helpful comment on a text of Scripture -- especially if the text is very common, or rather obscure -- I'll note in the margin one of two ways. Here is an example of each. (#1 is from Jer 17.1; #2 is from Jer 20.10).
#1. By writing in the quote:
17.1: "Sin, not law, was written on the heart - hence, the need for the promise of the new covenant." (Cf. 17.9) Ferguson, The Holy Spirit, 166.
#2. By writing in the citation, because the paragraph/section as a whole is helpful.
20.10: cf. Edwards, II.343 (Feb 10).
I always note the text in underlined format; not sure why, but it's consistent and clearly distinguishes where I'm working. Certainly, there are instances from time to time where my citation/quote isn't so helpful now as when I initially added it; but my aim was very simple from the outset: to collect insights for texts I had heard preached many times, and especially for texts I had not heard/read much on at all.
Thankfully, the discovery of irrelevance has been infrequent; and the Lord has helped me to develop the discipline of reading with pencil in-hand. I showed this method to my intern and our elder candidates because it has been so helpful for me.