I have a notepad (physical pen and paper), where at the end of a tiring day, i sit in bed and strategise how to place my workshop/piles in a way that makes sense... I've almost gone crazy trying to work out how to do this effectively and elegantly. I can't even begin to describe the problem from all the different aspects you'd have to consider when designing workshop/pile interaction.
So for simplicity, I do 3 layers, wood + stone (furniture, stonecraft), metal + gem (weapon, armor), plants, leather, refuse + food (meals, drinks, clothing industry, leather armor, bone bolts/crafts).
I used to separate out fish, meat, prepared, drink, now i dump into one pile. I separate out the dimple cup, pig tail, dyes, thread, cloth to see their supply level because i still have to manually kick off dye thread (haven't found the workflow command for that), when i do, i'll pile all these together.
My furniture industry is automated, set to produce 20 of each type and keep that level in stock for incrementally building bedrooms. that level just has furniture, maybe blocks.
My coal/bar industry is also automated, so i can just make weapon/armor using j-m manually. that layer has metal bar, coal bar, ores, all metal weapon, armor.
Food industry is fully automated, farms on top with seed bags pile. Food and refuse pile on a layer with kitchen, still, butcher, tanner, fishery, craft(bone). They are set to basically produce infinite food, drink, bone bolts.
Clothing is a pain... really complicated atm