Depending on how much you like to automate your fort, you will want more stockpiles. I like to have a rock stockpile, at least one wood stockpile, a cloth stockpile, and a designated furniture stockpile. Furniture shouldn't be too far from the (jeweler/mason/carpenter) workshops. The nice thing is that as soon as you have a stockpile for one or two specific items, any general stockpiles you have no longer need to accept that item, so they should be less cluttered. In practice, start with a general stockpile and begin specializing them out as you build your infrastructure.
You can also use stockpiles to customize some of the agricultural jobs. For example, create a stockpile for empty pots, a stockpile for pig tails, a still, and a farmer's workshop. Link the two workshops to the stockpiles as necessary, and create a work order for each one (disable general work orders). You can set the still to brew 8 plants once you have 12 pig tails, and the farmer's workshop to process 4 plants (or whatever ratio you wanted). Since you can't designate material for these jobs like you can with the mason workshop, I find this to help some. Admittedly it means a bit more micro, but it's invaluable if you're on an embark without above ground crops (such as a glacier) and want to maximize the return from the crops that you do have. A good compromise would be "this is my mill stockpile, this is my brew stockpile, this is my process to thread stockpile." Although if you do give this a shot, rename your stockpiles and workshops.