While this would work for the one domain, I believe the original poster has multiple domains and wanted a situation where SSH would automatically CD to the correct domain directory, depending on the domain (hostname) he used for the log-in. Of-course, they could expand apon your suggestion by creating a unique user to control each domain then modifying each users bash profile.
As for FTP; I think this is probably the easiest to configure, but it will need to be done at the client, not the server. Simply create as many site log-ins as required, in the clients site manager, and configure each with a different remote path.
Overall, I think it is all more hassle than it is worth.
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