Hello,
1 : Uninstall any traces of SQL Express through Add/Remove Program.If you are not able to remove it through Add/Remove, download "Installer Cleanup Utility" and remove SQL Express. http://support.microsoft.com/kb/290301
2 : Open the Backup Exec CD and go to the Install\SQLExpress folder and Install SQL Express seperately with default configuration
3 : Start installing Backup Exec by clicking on "browser.exe", it will prompt you for SQL Instance, select existing instance and point towards already installed SQL and continue installation
Hope this helps....