I want to set up 2 instances of rsync with different functions.

First, I want the traditional remote backup: nightly and weekly backups of certain directories copied over ssh to a second computer (I assume originals will be on the server end and the backup machine will be the client, using ssh to fetch the data).

Secondly, the machine with the backups is also an ftp server. I have previously mounted whole hard drives in a shared folder (/home/ftp with folders like upload, stuff1, stuff2, stuff3), but I want to use rsync to create hard links (no copies, just links) so I can, say, have the contents of stuff folders 1-3 in a new folder just called stuff and then periodically reload the links as changes occur in the original folders. I thought about just making a script for nightly "cp -la", but it wouldn't check for stuff being deleted.

How do I distinguish between backup and strictly hard links with rsync?

You can't make hard links across file systems. That is you can't hard link a name on one partition to a file on another partition or hard drive.

You know, that thought crossed my mind last night. Thanks for the heads up.