Yeah it really depends on your DE. They have their own display settings, which usually overrides any xorg.conf setting.
I.E. if your mint is with cinnamon DE, you can first do the settings you want with nvidia-settings. After that you should open DEs own display settings prog(menu->display). Click detect displays, apply and finally save configuration. Of course you don’t even have to use nvidia-settings for it at all, you should be able to use that DEs own display setting for it.
If my memory servers me right, gtk flavored DEs stores their display configuration to file ~/.config/monitors.xml(I have kde myself, so I can’t be sure about it).