Hello,
if you can use the same profile/cofiguration for all folders:
-configure one folder (and test it)
-on GeniusConnect ->"Synchronize Schedule" Tab, set direction for the folder to "Store All" and set the scheduler to "Extern scheduler" (you don't have to config a real scheduler!)
-copy the configuration from the template folder to all other folders (GeniusConnect config->Database Tab->select the source folder->"Copy Profile button.."
To Start the scheduled sync manually go to GeniusConnect installation folder and start "GCScheduler.exe", this will trigger the sync.
If you are on Exchange/Office 365 make sure you are running in cached mode.