Hello hello, welcome!
Personally, I don’t take any WK notes. I trust the SRS - if I don’t know, I fail an item and read through the mnemonics again.
Some of the user scripts, like the self-study quiz combined with the Extra Filters can be a great addition to learning.
These two together mean you can quiz yourself on leeches (words that you just keep getting wrong) or quiz yourself on the items you got wrong in your most recent review. Very useful.
Not saying you shouldn’t take notes, and I know a fair number of people do, but I’d say: consider the beginning of WK as a time to tweak what works for you. Don’t get too hung up on doing it one, certain way.
Taking notes on thousands of kanji and vocab is hugely labour intensive. If that works for you: perfect. 
But if you find that you’re burning out and avoiding WK because you’re overwhelmed at the amount of work: try to do things a different way.
Hope to see you around more, and good luck on your kanji journey!