Okay, this may make your brain hurt!

On application installed instances of SQL Server 2005 Express or Embedded edition, you cannot connect to them or manage them with commandline or SQL management studio tools.

But you can connect, using windows authentication, if you set the server\instance to: \\.\pipe\mssql$microsoft##ssee\sql\query

It’s kind of important because if the server isn’t backing up the embedded app dbs, the transaction logs will overrun all your disk space. And the OS/Veritas can’t back up the instance because they don’t know about the \\.\pipe\mssql$microsoft##ssee\sql\query connection string…

Sharepoint and other web applications that use the embedded SQL have their own web-based backup/restore tools that talk to SQL, but at least in Sharepoint, there is no scheduling component for this as of WSS V3 (possibly in MOSS or Sharepoint 2007).