As I wrote, you have to use an MSDE or SQL instance of some soft with BE - if you can't use this for whatever reason you have, then you will need to look at other backup software.
As I said, BE will NOT use the existing instance of MSDE, it will create a new instance called BKUPEXEC and use that.
I know of alot of customers that do this without any problems. It is actually why MS designed MSDE and SQL to be able to be installed into different instances, so if something goes wrong with 1 of them, the other should still be working OK.