The @media css will always apply to the set screen size, regardless of what else you put in the Custom CSS admin area. This is because the css for @media is nested and requires the screen size (768px in this case) to be encountered before it is applied.
I hope that makes sense.
To be honest, I put all custom css in the plugin area anyway, and just use child themes for adding to functions.php etc. I find it much easier than editing the child theme css via FTP.