When I enabled iCloud Desktop & Documents, the Mac I first enabled it on - my MacBook - uploaded all the files to the Desktop and Documents folders, respectively.
When I enabled it on the second Mac, its content was placed in a "[Brookzy]'s iMac" folder that was created in both the Desktop and Documents folders.
Personally I didnt want to separate them like that so I just moved the contents of the "[Brookzy]'s iMac" folders to the main folder, and now a single Desktop, and a single Documents, folder syncs between my Macs.