It's too early to say for sure, but I think I've figured out a way to organize my todo lists that actually fits how I work and doesn't require too much effort to maintain and stuff.
Instead of organizing the top level by project (e.g. a "yakread todo" note, a "biff todo", a "writing todo" note etc), I have two fixed categories: main and alt.
Main contains stuff that feels "high leverage", regardless of what project it falls under. Alt contains stuff that probably won't have a big impact in the short-term but that I still want to make some progress on. So far (about 2 days) this has made it feel easier to focus on the essential stuff and not have my main todo list get crowded out with too many items.
I try to keep each list to 7-ish items, and each item can branch out to a separate note with 7-ish items etc. So for any given note I can prioritize the tasks without too much effort.
I have found that using google keep for the notes is essential so that I can organize them on my phone.