Hi there!
Thanks for contacting us.
There are several ways to put custom codes. It depends on which method you chosed before.
https://www.joomshaper.com/documentation/helix-framework/custom-code-css-js-meta
Custom CSS field of the template options or custom.css file? Yes, you need to change the codes for each and every copy of your template styles.
Moreover, if you put custom code specifically in a section of any page, then you need to be specific for that saction by manually putting the code there, or you can find unique selectors and put the code in your custom.css file either.
Hope this helps anyways.
Best Regards