To copy all files and folders on S: except for S:\foo\ and S:\bar\, check the Filter box and enter \foo\ ; \bar\ into the Exclude field. Omitting the leading backslash will skip all directories named "foo" or "bar", regardless of location.
Options to review when enabling the filter: Option > Main Settings > Copy/Move Options > "Don't create empty directory, if 'Filter' is checked." and Option > Main Settings > Delete Options > "Try to delete directory, even if 'Filter' is checked."
Delete files and folders unique to the destination by changing the operation mode in the dropdown box from the default "Diff (No overwrite)" to "Sync (Size/Date)"
Appending a backslash to the target directory will result in a new directory being created therein.