How do I turn it off?
I went to save, and found both of my previous manual saves had been overwritten.

You can turn it off by interacting with the sparkling book next to your bed in the castle in Aldlyn.
The auto-saves save all 2,5mins alternating between save slot 19 and 20.

That explains why my saves were overwritten.
I always save my games starting at the last slot working up, because everyone else I know starts at the top, to reduce the likely hood that a friend may overwrite my save data.
The exception being Skies of Arcadia, if my memory is accurate. I recall that game initially only having one save slot, but if you save to it, it then has two save slots… Due to how its save slot features worked, you could only work new saves in below old ones.

Thank you for your help.
If I turn it off in the current file, it will continue to stay off if I delete save files 18, 19, and 20, right?