Followed  the instructions at http://technet.microsoft.com/en-us/library/cc512723(v=office.14).aspx

Moved all sharepoint databases to a new server.

I left the SERVER_NAME\SHAREPOINT instance installed on the SBS 2011 box but have found that backups are failing because Backup Exec is trying to access the databases through that instead of through the SQL Client Configuration which interestingly has an alias named "SERVER_NAME\SHAREPOINT" that points to the new server. (A heap SQLVDI errors etc).

So on the SBS 2011 box I went into control panel

1. Un-install a program and
2. selected "Microsoft SQL Server 2008 R2 (64-bit)" and
3. right clicked and chose "Change/Uninstall"
4. selected the Remove option
5. Waited for the validation step to complete
6. Selected the "SHAREPOINT" instance
7. Selected "database engine", Full text and something else I can't remember
8. Clicked next till the end.

This removed the SHAREPOINT SQL instance and stopped Backup Execs confusion as to what SQL instance  needed to be backed up.