[eluser]John Fuller[/eluser]
Do whatever makes sense to you. I think running the admin and the front-end as two (or more) different applications makes total sense. You can setup symlinks to share resources. Another possibility is to setup central resources and have external applications communicate with the central application via XMLRPC or whatever you want to use. Even if you do have the duplicate libraries, setup a master and then shoot your changes through your network using Rsync. Use your tools, dude!