If you have already created a connection profile then right click on profile and select ‘Edit profile’ option. On Edit Connection Profile dialog, click the 'Configure' button under ‘Files and Folders’ section.

Then check ‘Select the folders to exclude’ option and click on 'Exclude Folders' button to choose the folders you want to exclude from the transfer. Click Ok and finish the settings.

Now, whenever the automated transfer runs the excluded folders will not be transferred.