I finally found out how to do it.
You need to map each user's folder onto an already existing folder in your domain. Go to your control panel and click on "domains" and then "Remap sub-dir."
Select your domain from the drop down box, and in the next box enter the name of the sub-directory.
On the next page, select the user from the drop down box, and in the next box enter the name of the subdirectory if there is one.
Anything that's uploaded to home/username/folder will now be accessible via the web at www.yourdomain.com/subdir