Throughout the day, upon conceiving (while meditating, reading, whatever) a thought that deserves inclusion in your graph, search for a good buffer for it to belong to. If that buffer doesn't exist, create it. Either way, after recording[1] the idea, leave the buffer open. At the end of the day, read through those buffers, boundedly depth first. When one becomes boring, close or bury it, and continue reading.
It is an integrative experience.
[1] Add to the top of the buffer (prepend) by default, unless you've got a good sense for what else is in the buffer and believe what you're adding generally underranks them. This causes your review to be roughly ordered by recency.