In principle you can have as many sources as you want.
For now, this kind of filtering is not possible, but you could retrieve all files with an FtpSource and then use a Router (or a MessageSelector) to send them to different handlers for processing. Of course, this currently has the major inconvenience that will still retrive *all* files, regardless whether the intent is to process them or not.
Please follow on http://jira.springframework.org/browse/INT-294 as we intend to improve the functionality in this respect.
Spring Integration Committer