User Documents are what is placed in the root folder of the server. Its the top path in the server settings tab.
These you can use for controlling static documents, which access rights you don't need to alter.
Source documents are documents placed in one of the folders mounted in the distribution resource settings. Here you have master documents, that you set to reload and copy to one of the mounted folders on the server. This option is only available if you're also are running the publisher. In the copy process you're able to set access rights on the documents, and distributed them based on reduction rules.
I do agree that this difference is a bit annoying, and I think that QlikTech should get rid of User Documents, and simply remove some functions from the source documents model if you're running publisher. No larger installations use User Documents, and the smaller are forced to use them even though they prefer not to.
Rather simple really ... User Documents are delivered to Users by QlikView Server, and Source Documents are managed by Publisher (QlikView Distribution Service). With a Publisher Licence, you may have some documents that perform Extraction from Database to QVD, or other master documents thatr end-users do not see. Finally your Dashboards would be reloaded as Source Documents and Distributed to a User Document folder for delivery to end-users via AccessPoint (though Publisher might also mount the User Document location to perform reloads in-situ without a distribution task).
Without Publisher there is less distinction, and actually Publisher simply mounts the User Document folders. Distribution tasks are not available, so back-end documents are concealed from Users simply using the Document Security Model (NTFS permissions).