For plants-to-mill-into-dyes
Set the stockpile to be a food stockpile, then hit 'b' to block (forbid) everything. Go to 'plants' in the middle list. In the right list, scroll UP to wrap around to the end of the list. "Dimple Cups", "Hide Root", "Blade Weed", and "Silver Barb" are all together at the end of the list. Hit 'return' on each of them to enable. You now have a stockpile that only allows dye plants.
Back in the q-select for the stockpile, click 'g' (for 'give'), and it will prompt you to select (via moving the cursor and hitting return) the stockpile or workshop the stockpile should give to. Select your dye-quern.
For bags:
On a furnature stockpile, 'f' for 'forbid' 'type' from the middle list. This forbids all types of furnature. Then, find "boxes and bags" and enable it. [f]orbid all of the material type items in the middle list. Then, in the right-hand list for 'other materials', turn on cloth, leather, yarn, and silk.
same procedure to link it to your dye-quern.
Note that as others have indicated, once you link a stockpile to a workshop, that workshop will ONLY take items from stockpiles that link to it. It took me forever to get a dye-only-quern working, because I didn't realize that once I linked a plant stockpile to it, I would also need to link a bag stockpile to it.
You will also want to set your dyeworks bag stockpile to [t]ake from your dye workshops, to keep it a closed-bag loop. This means that you will also need to set a cloth/thread stockpile to [t]ake from the dye workshops, or else the dyed items will never be removed. Another quirk I tripped over: turns out that the seed created by the milling process is left in the bag rather than in the quren, and so it will get left in the dye-workshop when the bag is emptied. Therefore, if you set any stockpiels to [t]ake from your dye workshops, you need also to have a seed stockpile [t]ake from them, or the seeds will never be removed and will eventually clutter up the workshop until they are too full of seeds to be used (something else I figured out the hard way.)