For anybody using Stockuploader and not very tekkie (like me) this is what you need to do    :

Go to the config tab and add/edit the alamy agency in the normal way.  For STOCK photos, at the end of the ftp address, just add /Stock (so that the entire path includes the folder you want to upload to). This will upload all images to your stock folder.

If you do not shoot editorial or use releases you should be fine. If you need to upload editorial images or releases you need to add a NEW agency with the proper folder in the ftp address.. So you could end up having 3 agencies set up for the one site. One for uploading editorial, one for stock and one for releases.