For stash organisation, I use a two pronged approach:
1. A general 'inbox' stash. This is where I quickly dump stuff when I'm running targets/areas using the GoMule features of 'Pickup From... Stash'
I only use this inbox for general running - not specific projects. In many cases this is the only stash I need to update - meaning Flaive reports are very quick when generating report files.
2. Then I'll periodically sort out this stash in a more granular fashion - I have recently updated my stash organisation, but there are too many to fit in a screenshot...
I separate stuff based on item groups (Normal, Exceptional, Elite), Sets, Uniques, Rares, Open Sockets, Plain White, Rune Rroups, Quality of Gems, items for a specific character, items suited to a class, and combinations etc.
Although I make heavy use of GoMule's filtering capabilities, I find smaller stashes easier to maintain and allows for ATMA usage too.
I like having character stashes too, this is where I put future items earmarked for a certain character in a stash ready for them to grab when they reach the right level. This helps me keep track since I have so many characters and saves me searching for something.
I use separate projects stashes for things like the untwinked 99er. In time, I'll split Durnik's stash into things I plan to use in the future and another stash with item finds etc.