From version 1.0.2 onwards, EasySync allows you to sync multiple folders at the same time. All you need to do is to drag-and-drop multiple folders onto the drop screen.
When syncing multiple folders, remember that the sets of folders must match, so for each folder on the left, there must be a folder on the right with the same name. If this isn't the case, EasySync won't be able to tell which folder to sync to which folder.