My native theme options keep overwriting my custom code!

I have custom code for the header of wearabl.com - it fixes the header at the top of the page during a scroll, but it gets overwritten when I save any changes using the native theme options.

What can I do to prevent this?

Here are the two fixes tweaky suggests:

1. Adjust custom changes so that theme style settings can be adjusted through the native options

2. Move custom header changes to a child theme

What do you guys think?