The bad thing about downloading your files with an FTP client from your FTP account is that when you download them o Windows OS and upload them on some other host or the same host, you change the user of the file, you usually alter the permissions too, thats why sometimes some thing might stop working because you don't have permissions to write to a file, to upload a file through your CMS and things like that..
If it's possible, even though I never did it, it's best practice to backup everything through some Control Panel which has a backup feature which later could be uploaded with the right permissions and user rights, but I guess there's also some bad things about it which can happen.. Best way if you have your own CMS or you're using some kind of CMS is to have a backup feature if the Control Panel feature sucks.
Another good choice is to have a lot of your data in a DB which can be easily backup-ed, but in general it's much better to upload images as filenames into the server and not into the DB, permissions can always be a headache, especially because PHP and FTP users are different !!!!
To add, Yes as I remember the Logic plan only offered 1 MySQL DB, that was the reason I didn't really like it and changed to Pro, if it offers 5 Databases now, when it's really GOOD.
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