To change those settings, you have to enable the Advanced Mode first.

You find the setting within the expert settings.

There you can may deactivate the checkbox at "Synchronize available folder automatically". If you do so the client won't set up any new folder that can get synchronized automatically. Folders that are synchronizing already won't stop only new folders are afflicted.

Also you have the option to deactivate the automatic upload of new folders in the base path. For that you just need to deactivate "Auto-detect new folders in the folders-basepath".