My preferred organization method is tags instead of groups (folders)
I prefer tags because multiple tags can be assigned to a note
which even supports different structures at the same time
I reflect hierarchy in my tag-names; for example
Budget-Housing, Budget-HousingRent, Budget-HousingUtilities, …
My top level tags are Type-aaaaaaaaa
which drives additional tags
For example Type-Receipt items also have tags for Vendor and Budget-Category
I use an applescript to assist with tag assignment