I have two different Macs (15" Retina MBP Mid-2012, 27" 5K iMac Late 2014) that I would like to sync my Desktop & Documents Folders using the iCloud Drive features in macOS Sierra. By just turning on this feature for both Macs, it has created duplicates. The MBP, which was synced first, appears to have populated the Documents folder in iCloud correctly. The iMac, which was synced second, created a folder within the Documents folder on iCloud entitled "Documents - iMac."
From what I read here and elsewhere, it appears that the feature is not intended to merge (and offer to resolve conflicts with) sets of data that originate from multiple Macs.
There's an earlier topic – iCloud Desktop and Documents Duplicates – but I don't know whether what's there is applicable with golden master candidates.