Every enviornment is different so determining what is the right configuration for your company needs would be tough. SQL supports Full, Transaction Log and Differential backups. Transaction Log backups are the only backup type in SQL that will perform Log Truncation. For databases in a Full Recovery Model, you are going to want to schedule Transaction Log backups in order to keep the size of the LDF file manageable.
Full Recovery Model allows for Transaction Log backups to be taken. More frequent Transaction Log backups would give you better Point-in-Time recoverablity.
Simple Recovery Model does not support Transaction Log backups because it manages its own log truncation.
As far as subclient configuration, the default subclient is going to be the "Catch All" Subclient and will discover new databases at the time of backup as they are created on the server.
The subclient configuration you mentioned isn't a bad strategy as it would allow you to schedule the System Database, Full Recovery Model Databases and Simple Recovery Model databases differently if desired although CommVault does have a built-in set of conversion rules that help with single subclient configurations.
If you do not want CommVault to convert according to these rules, creating subclients as you mentioned would allow you to schedule different Recovery Models differently.
Below is some additional information from Microsoft on SQL Server Backups.
Backup Under the Full Recovery Model
Transaction Log Backups
CommVault Messaging Support