Stockpiles are normally split into broad categories, as you've discovered (food stockpile, stone stockpile, etc.), and these can be further configured and split into narrower (and broader, e.g. stone AND food... though I don't know why you'd want to do that) categories and sub-categories by altering an individual stockpile's options, just as you'd reconfigure a workshop ([q]).
Stone stockpiles can be configured to accept/deny Metal Ores, Economic Stones, and all other stones that don't fit into either of the other categories. Ores, you know about. Economic stones are non-ore stones that still provide additional uses beyond masonry (currently these are "flux" stones used in the production of steel, and gypsum-like stones that are used to make plaster powder). Note also that obsidian and bauxite are normally listed under "other" stones, but also bear distinctive qualities (obsidian can be used to make sharp blades and is more valuable than "plain" stones, and bauxite is well-known for being magma-proof).
Use of specific stones can be restricted via the "Stones" submenu (under the status screen ([z])), which toggles whether dwarves can use them for any jobs, or only for their specialised purposes.
Foods can be configured in a similar way via the "Kitchen" submenu, which broadly prohibits use of certain food items (including seeds) in brewing or cooking (not that seeds can be brewed, but they can be cooked... not sure why you'd want to do this, except to eliminate rat weed from your stockpiles, though you could just dump it). Saving your dwarves from a lot of legwork, though, comes down to stockpiles.
MY approach is generally to have a stockpile near the dining hall that accepts prepared foods ([ u ] toggles this), but not seeds, fat, extracts (like inedible Gnome Salve) or other liquids (lye). A stockpile near my farms accepts only seeds, a stockpile closer to my farm workshops and quern/millstones accepts the plant products (sometimes further subdivided, if they are more distant), a stockpile near the still that accepts brewable plants (any idea why it's called a
still if it
brews?) and maybe another for excess barrels, and another near the kitchen that accepts unprepared fat, tallow, meat, "cleaned" fish, and processed plants i.e. quarry bush leaves, cave wheat flour, dwarven syrup etc. You needn't create so many different "food" stockpiles, but I find that it helps speed things up a little.
If you want to separate food and drink, you'll need another stockpile: forbid drinks in one (stockpile settings, [q]) and forbid all other food items in the other. Should do the trick.
As for masons, make sure that the stockpile(s) near those workshops doesn't accept stones that you don't want being turned into furniture/blocks: [q] and change stockpile settings as with your food stockpiles, it's that simple. Dwarves can be forgetful, though, so if you want to be doubly-sure that a mason won't pick up the copper nuggets he's standing next to while on break near the smelter and take them off to make a -copper nuggets table-, set prohibitions via the Status/Stones menu (by default, all ores are "prohibited" except for special uses, likewise economic stones unless they make up the majority of stones on the map... I once started a fort on a mountain that was nearly all-dolomite (flux) and its use for masonry jobs was automatically enabled (40d), but since it was so plentiful I didn't really mind).
Unfortunately, there isn't an "easy" way to tell your jewellers/metalsmiths/leatherworkers/etc. to encrust or otherwise enhance
specific items, so you'll again have to be crafty with stockpiles (since dwarves generally use the closest available items to complete a job). Create a stockpile near your jeweller's workshop that accepts e.g. only thrones of a certain quality and made of a certain material, and he/she should eventually get the picture, although the first attempt might not be what you were aiming for if they had to get to the shop from elsewhere in the fortess (when getting my dwarves to make magma-proof stone items, I typically need to rig at least one "dummy" job at the mason's workshop to get my mason over there, after which the next job (construct rock floodgate WITH THE BAUXITE THAT IS RIGHT THERE) actually gets done, so a one-off piece of bauxite furniture actually costs 1 bauxite, 1 "junk" stone). OR, you could temporarily restrict a dwarf to a burrow that encapsulated only the workshop, the cut gems, and the item to be encrusted, but I haven't tried this, yet.
As above, you can't specifically order a brewer to make wine-and-not-ale, for example, except by forbidding ale-making plants or prohibiting their "brew"-ability through the Status/Kitchen menu. The other way to do it, which won't outlaw ale production at all, is just a method of encouraging wine production over ale by situating the wine-plant-accepting stockpile closer to the still than the ale-plant-accepting one. That way, when your brewer finishes making a batch of (whatever), he's more likely to grab the plump helmets that are next to him to fill the next barrel, than go off to the other end of the fort to get those pig tails.
Hope that helps :S
jew shop
wat.