The current version FileManager doesn't allow synchronizing a folder and its subfolder(s) at the same time. For example, if you have a local folder:
"C:\A\B\C"
And if you have synchronized "C:\A" with a folder on DriveHQ "\A", then you cannot synchronize "C:\A\B" with another folder on DriveHQ "\B". Note the folder "C:\A\B" is already synchronized with the folder "\A\B" on DriveHQ.com.