Cloud feedback is not just "added" uncertainty; it has the potential to completely stop global warming in its tracks. Please note that I said that.
At the same time, cloud feedback may NOT have the potential to stop global warming in its tracks. That's because it's uncertain! The cloud feedback from global warming might be a negligible factor; that would not be good.
Despite the fact that weather does distribute water vapor, weather is predominantly tropospheric. The positive water vapor feedback concerns the increase in relative humidity from the bottom of the atmosphere to the top.
As this brief link illustrates, http://www.sciencedaily.com/releases/2002/02/020221073102.htm, stratospheric water vapor is still primarily a weather phenomenon (especially if you count changes in the jet stream). Certainly convection plays a major role and topography is also critical as shown in this link: http://www.pnas.org/cgi/content/abstract/103/15/5664