So - I fully understand the need to have all stones moved out of the way and the fortress neat and tidy with everything in its place.
What I do is minecart quantum piling. Pretty much the first pile I build, right after a carpenter knocks out a mine cart as his first job.
You set up a modest stock pile, say, 3x3, for stone (or anything and everything you want) - if it is for stones or heavy things, include some wheel barrows. Dwarves will fetch stuff and bring it here, but at 9 spaces, it will be full very quick.
Next to this pile - the input pile - I build a track stop, set to dump to a square outside the input pile. I set another 1x1 stockpile on that output space, set to hold the stuff. I designate a hauling route with a single stop, on the track stop, assign a vehicle, and have it take from the input pile the things I want (but not wheelbarrows, that is important)
Now dwarves will grab things in the input, stick them in the cart, and they'll dump into the small pile. Dwarves will let them stay there as they are in a legal stock pile. As they empty the input pile, dwarves will go fetch more things. Eventually, everything winds up in the small output stack, all neat, and all automated.
There are two things to watch out for - one is if your piles handle wheel barrows, they'll get eternally shifted, and the other being barrels that have something in them, which just don't seem to work - so don't use this for booze, or for food/seeds that are in barrels (you can use non-barrel held food, and seeds in bags (but not seeds on their own, dunno why)
also, if you mess up and have the cart dump into the input pile, dwarves will for ever load the cart with the items being dumped straight back into the input in an eternal cycle.
Anyway - this is useful for stone tidy up, and for above ground towers where space is a premium. Have fun