I think you work for a certified Datawatch partner? Have you received any product training on Automator? I think it might be an idea to have a work with your partner manager at Datawatch and try and get something organised.
Automator can (if you give the service account the credentials) access web resources like Modeler can and retrieve files via http, or https. You can also script Automator to run an ftp or sftp script before executing the process.
Processes can be scheduled. If you want to run a null process that just fetches the document and then passes it to a third party application, just use an input distribution.