What is backup?
Backup lets you define specific folders that you want Jottacloud to "watch", by dragging the folders into the "Backup" tab in the Jottacloud desktop client. The software then tries to "mirror" all changes done to data in the these folders, uploading any new files added, uploading changes to files and deleting files that you delete. All downloads from these folders need to be started manually.
What is synchronization?
The syncfolder (default folder name: "Jottacloud") does the same as backup, but in addition it tries to synchronize the contents of the folder to all the devices registered with the Jottacloud account. This means that a change done by one of the registered devices to contents in the "Jottacloud" folder, will be uploaded to the server, and then downloaded to all the devices connected (as long as the client/app used on the devices supports sync.).
You can also share folders that are stored in the Sync folder. If a folder is shared, it will try to synchronize all contents and changes to all the members of the folder.
Where should I put my folders?
We usually recommend that you put the folders which you want to share, or need immediate access to on all your devices, in the syncfolder. The data you just want to safely backup, should be added to the Backup tab in the desktop client.
The reasoning behind this is that it is very easy to use up a lot of harddrive space on your connected devices, if all data is put into the syncfolder.
Is there anything else I should be aware of?
You cannot add the same folder to both the Syncfolder and Backup, you have to choose one of the systems on a per-folder basis. If you for some reason want to put a folder from Backup in the syncfolder, you have to copy it and give it a new name.