Backup Exec (BE) uses a SQL instance.
Backup Exec System Recovery (BESR) for Desktops or for Servers does NOT need SQL of any kind.
However BESR Management console does need some sort of SQL (can be Express.). As you're pretty much deploying a full Altiris server.
That said, They should be separate. Why? It's not because of SQL..
It's because the Altiris management console only runs on 32bit, and BE runs best on 64bit for performance and for compatibility reasons (Exch 2k7 and Exch 2010 and Dedupe).