You don't say if you are intending to upgrade the Backup Exec SQL Express instance to full SQL 2005 or whether you just need another SQL instance for another application?
However some comments:
- SQL 2005 and SQL Express instances installed on the same system are only an issue if Microsoft indicates there is a problem. It should not directly cause an issue with Backup Exec itself
- Backup Exec can run in a full SQL 2005 instance
- It is not recommended to run Backup Exec database out of the same instance as any other applications
