SQL Server backup media set and file separation
I would say that there isn't necessarily a Best Practice, this is more of a matter of personal preference or your businesses operating procedures.  I've had separate folders per database, then sub folders for FULL, DIFF, LOG at some jobs, others everything goes to a single folder and the backup name is some combination of database name, backup type, and datetimestamp to make each file uniquely named.  I'd recommend looking at Ola Hallengren's maintenance solution: 

https://ola.hallengren.com/

This is what I recommend to all my clients for database maintenance and backups and it handles everything dealing with the file naming and folder structure automatically for you.  Just run his script and set the jobs to run at the frequency and schedule that meets your requirements and you are all done.