This is sort of messy to explain so I will use images to help.
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A is a stockpile that accepts any stones, rough gems, metal bars, coal bars, and sand bags.
B is my dump pit and at the bottom is a stockpile that accepts everything dumped by A and C. The door is locked while things are dumping.
C is going to be two stockpiles set to accept from the main food stockpile and will be linked to give to the dump pit via cart.
D is my Furnace QSP input set to accept only from links and linked to the smelter and the stockpile at the bottom of the dump pit. It only accepts ore stones, clay, sand bags, metal bars, and coal bars.
E is my Furnace QSP. It accepts ore stones, clay, sand bags, metal bars, and coal bars and is set to give to all the magma furnacs.
I will tweak the dump settings on C so it only happens every other month or twice a year or something or throw in a door and lock it so that it only happens when I want it to. Are there any obvious issues where this set-up will fail horribly or get stuck in a loop or lead to other forms of FUN I haven't considered? I also have two burrows on for everything on Z-levels 0, -1 and -2 and one for everything below that (basically stairs and Z-28) that I plan on putting all but my miners into for the moment. So my miners will be able to grad empty barrels and finished goods.
I have 8 dwarfs and will receive no immigrants so I have plenty of time to expand and having my miners hauling won't be a big issue.