To get clarity, please correct me if this is not accurate:
Version: CRE Loaded6 v6.2 B2B White Label[13.2 (SP1)]
The version should not matter. The complete backup facilities should be the same across all currently supported versions.
Backing up the database is done by Admin->Tools->Backup mySQL which is the same as Admin->Tools->Database Backup?
This is not the case. Backup MySQL depends on access to the MySQL command line tools and to the PHP functions which allow processing a system command line. Neither of these conditions is guaranteed to be met on any given server. This is why there are two backup tools. The Database Backup tool uses PHP to generate the backup. This works across more servers, but is limited in the size of database backups it can manage by various Apache settings which, when set liberally enough to allow management of large databases, increases the risk of and vulnerability to denial of service (DoS) attacks against the site.
This has the Cre Loaded Admin user accounts and passwords in it. Upon restore, I would lose any new accounts or password changes done since the backup that I restored, along with any new catalog items!
True. This is why systems such as FDMS have their own partial backup systems, and why that approach will be extended to other systems during the course of EOS development.
The website files and most modifications are not in the Database, they are in the file structure on the web accessible directory (usually /public_html/).
True. cPanel and other hosting control panel systems generally offer automated methods of creating such backups as quicker alternatives to FTP retreival.
Where is the mySQL database typically kept in terms of files?
The MySQL server generally manages this, and the actual database files are rarely if ever owned by the site owners system user account. This means you just don't get to back them up directly. Instead you must rely on your authorized access to the database and tools such as your control panel, PhpMyAdmin, MySQL Administrator and so on.
David