How to customize duplicate site without affecting live site?

Made a duplicate of the current site to add new theme (Elle theme) where we are currently adapting the site in order to eventually publish but we can’t since the apps we use have been customized in the current live site for visual elements we needed to adjust and they can only be done by editing the .liquid files.
Not only apps but also product page fixes that we can’t do there, quick view fixes as well, navigation, etc.
How can we fix these issues without publishing the unfinished new theme and without affecting the current live site?
Thank you