How to Organize Storage and Stockpiles
Separate stockpiles for any goods you expect to handle in large quantities. You don’t want to find out you’re running out of your primary alcohol of choice, or cloth, just because some other underused crops’ seeds exceeded your shared stockpile settings.
This applies to basically anything that’s part of production chain. Final products can be handled even if they clutter workshops without much disruption, but if some base or refined resource has its supply disrupted, that can result quite quickly in all manner of !FUN! situations.
Personally, I set up smaller “work” stockpiles to handle the flow of production as close to appropriate workshops as possible. Priority being the ones that use them as source, output workshops being a bit further away can be handled by haulers. Preferably, though, you want “production clusters” of appropriate workshops to be as close to each other (and the work stockpiles) as possible. Then I set up larger “long-term storage” stockpiles elsewhere (generally one or two z-levels difference from the production floor), with the work stockpiles linked to replenish from those when low.
Ultimately, you want to slowly create individual stockpiles for most things. You can start by categories (say, one stockpile for seeds, another for meat, and so on), but any goods you’ll be handling a lot absolutely should be separated as soon as you start setting up dedicated production around their availability.
One you get comfortable enough with the basics, things like quantum stockpiles are extremely helpful, and setting up even half-automated mining cart system for moving things between sub-sections of the fortress makes things even more efficient.
There’s a lot of automation potential in Dwarf Fortress (both in terms of gameplay and in-game use of automated systems), figuring those out is a lot of fun.
“Magma shotgun carts for everyone!”
Anyway… tl;dr: make lots of exclusive stockpiles for things you’ll be handling a lot, especially during production process.
Keep things tidy, and dwarf on.
In addition to what’s been said above, one tip I’ll give is to really dial in your furniture stockpiles. They contain a lot of goods that don’t fit in bins and will take up a lot of your space. Separating things so you have your actual furniture in one stockpile (maybe even linked to a workshop that decorates), things like sandbags in another, and empty barrels near your still/kitchen.
Having workshops that use each other’s good being nearby helps a lot too. Have your farmers workshop, loom, dyer, and clothier shop all nearby.
Make sure to use work orders to fine tune exactly how much stuff you produce.