Because Hive is in Documents on Windows, to avoid overlapping syncs you first have to disable Hive before you can sync Documents. To do so, open Preferences - General in the desktop application and enable the option "Disable the Hive folder on this device". Press OK. Completely shut down the application by clicking or right clicking on its icon and choosing Quit. Reopen the application. Hive is now disabled on that computer. Repeat this step on each of your Windows computers on which you want to sync Documents.
That's all you have to do, and you will now be able to create a sync that includes the Windows Documents folder. Some users also like to delete the Hive folder from the computer, using Whe Windows file manager. Other users like to delete SpiderOak's copies of the files in Hive from their account.