You've got three similar UI widgets that are totally independent: activity zones, stockpiles, and burrows. (Really, designating rooms from furniture is a fourth -- dining rooms, barracks, bedrooms, etc.) Confusion could be reduced by combining all three (four?) into one interface, the zone, using the current, and very nice, creation interface from burrows.
(As an aside, I hate the name "burrow," because burrows have nothing to do with digging cozy quarters and everything to do with confinement. To give an example based on my experience, one of the first things I created was a bedroom for my leader, and I made it his "burrow" because it sounded cozy and prestigious. And then I couldn't figure out why he never left his bedroom for a year -- he almost starved and dehydrated, and his skill set atrophied. I'm not saying what I did wasn't stupid, but it might be a good idea to discourage such stupidity with a better name. Here's my quick starter brainstorm: "work area," "workplace," "restriction zone," "work confinement," "confinement area," "confinement zone"...)
I like the fact that the three types are differentiated visually, but they are so similar in form that they should be created the same way, using the lovely mouse-based interface for creating burrows which makes it so easy to add or subtract individual tiles from individual zones. This would imply choosing one of the three types on creation: Stockpile zone, activity zone, or "confinement zone" (or whatever you want to replace "burrow" with). I would suggest remaking rooms defined from furniture as merely a specialized activity zone that requires the presence of that furniture.
The "q" key could then query everything, be it a building or zone. For overlapping zones, cycle through them with "q" the same way you cycle through overlapping units with "v". Also, fold "t" into "q".
In general, I justify my suggestions by saying that, since it looks like you might never stop adding features to DF, you may want to at least take a break from it to polish what you have already in terms of user-friendliness.