Best approach to maintain many dump for a single structure
Always the best practice is to take each database's backup with a separate file.
Why?

You can restore any database to anywhere.
It'll help to refresh you Dev database.
It'll help in PITR.
You can restore any specific table from the specific database backup.
Finally it will save a lot of time while restoring a single Database.

Recomendation:
Keep you database backup in multiple locations. This will help you in case of any disaster.

SAN
NFS
S3
Or any other location apart from the Database server.