I don't use DFHack though. I just play Dwarf Fortress straight out of the tarball, the way Urist intended. Well, I do turn off aquifers, but no tilesets! Tilesets are a sign of weakness. I tried Therapist twice, but gave up on it.
As for the stockpile idea, it doesn't seem to work right for me. I either end up with dwarves running out of the stockpile to grab whatever rocks they want, or I get piles of cancellation spam about rocks.
DFHack exists to compensate for the lack of features that Toady either hasn't gotten around to, or isn't willing to make. Toady isn't known for reacting to suggestions very quickly. If there's a solution to something that you can achieve with modding or DFHack, you're better off just using it. (No point suggesting crops that aren't broken, it will get fixed eventually, and there's mods that make them work...)
Anyway, I'd need to know more about what trouble you are having with your stockpiles, but basically, you should review the
give to/take from functions, as it's rather fiddly, and the interface has no method of giving you any help on why something is wrong.
In general, just make sure that you have only one stockpile set to "give" to a workshop, that workshop has the proper settings, it has "take from anywhere" and none of the other stockpiles accept the stone you want, or else you have take from stockpiles on stockpiles that are accepting those stones. You will probably want carts to haul stone from one stockpile to another due to speed issues.