I'm just beginning to wrestle with this. One of my main problems is how to describe burning and dodging in a way that I can come back to it months or years later and do the same thing. I've also just started split filter printing most prints, and that adds a new wrinkle to everything.
The snapshot of what I do now is that I use those black and white bound essay books with the empty, ruled pages. Each image I work on gets it's own page. I use the left pages as scratch while I'm working on a print, and record what I've done that day on the right-hand pages. On the back of each test print, after I've exposed it, I mark the filtration and exposure with a sharpee and wave it dry before it goes in the tray. I tried grease pencil, but that came off in the trays. If something might end up being a final print, I write in light pencil, but it's hard to see what I'm writing. While I'm refreshing the water in my print washer, I write down what I learned about how to print that image in my journal: the index number of the image, the date, what paper and developer I used, the lab's index number for the image (if that applies), enlarger elevation, which filters got what exposure, etc. Then, I draw a 2x3 grid, each with an outline of the image that I use for outlining where I dodge and burn and with which filter.
Seems to work well enough for the time being that I'm not motivated to come up with something different. I did just make one change last night, though. I started marking burn/dodge times as a percentage rather than a number of seconds. Seems easier to revisit for other sizes.
-KwM-