Hi Tess,
Please make a backup copy of your custom.css file because every single file in your theme folder will get replaced and after the update simply add the old content of custom.css to the new (in fact you should update via ftp, and just delete the old folder and upload the new one in its place and only then go into wordpress to ensure that the settings remain. However we strongly urge you to make a full backup copy of your database as well as the theme itself so that in case there is a problem you can quickly revert back to your current setup.
The Quick CSS will not be touched by the update.
In the future, please try to use a child theme so that you will not have to worry about overwriting anything.
Thanks,
Nick