Regarding the settings path:
I can only assume/guess (Jean has to confirm), but QAP need to resolve the OS variable?
If you want to control/override where QAP reads/writes it settings you may check out this
Can I set the QAP settings file location from the command line or a file shortcut?
For backups:
I use the same folder for the settings file and the backups, never had any problems with it.
Hope this helps.
Regards,
joeNOR