We have checked the synchronization with Amazon S3 provider and for our test account it's working well. We can get all files from this provider as you can see on a screenshot. To synchronize your documents you should enable this checkbox .
About "the Apply button doesn't seem to do anything" - try to reload the web page without cache (Alt + F3) or try to use other browsers . On our side we can't reproduce your issue.
Please follow our instructions and if you will have the issue again, then please share with us your browser version . We will investigate the issue and will be glad to help you.