first question is performance. If your BE server willl backup lots of remote servers and lots of data, the SQL server will be more sufficient than the MSDE.
The advantage of MSDE is, that it is selfmaintaining.
If you already have knowledge of SQL, you may well put your BE database on your SQL server. You should consider to create a seoerate instance for that, rather than just adding the BE database to an existing one.
Keep in mind, that the automatical restore of master db will not work for the instance, that holds the BE database.
regards
uz