Another thought is simple, set up a total of 2 new sections capable of being closed off per still...and probably a 3'rd nearby spot/room (dosn't need to be able to close off)
Now for how to work it...simple diagram.
|1|2|3f|
Section 3f is of course the 3'rd spot that is normally connected to the fortress.
Section 1 has the still, sleeping arrangements, and everything needed to keep the brewer happy and alive.
Section 2 is the intermediate area, that will be used for stockpiles..think of it as an airlock.
Section 3f is the fortresses section for exporting/importing.
Most probably get the idea of whats going on but I'll continue.
When the brewer is making his brew section 1 and 2 are open to each other, and closed off to 3f. Section 2 will have a stockpile that accepts whatever you want to brew (and of course will currently have the item in it). It will also have a stockpile that accepts the brews that the brewer makes.
When you wish to refill the area and take out his trade goods its simple. 3F will have one stockpile that accepts the items to make the brew out of. Close the brewer inside of section 1 (I'd suggest have a small stockpile inside for him to continue brewing if at all possible) then open section 2 to 3f. Now set 3f's stockpile to only accept brew..and 2's stockpile to only accept the items to make the brew with. Once 2 is out of brew and full of things to make brew with..close section 2 off from 3f..and open it back up to 1.
Very simple airlock type system. Now if you want to be fancy you can find a way using levers, water, and the like to push items around so airlocks are not needed.