Using environment variables in Github, NOT in actions

Question

I am working on setting up CI/CD for my organization. I am trying to build an automated system that will deploy our changes to our Shopify theme when we push to a branch.

I have a config.yml file that contains information like password, themeID and so on. I am trying to find a way to hide these variables in our repo. Github secrets have not seemed to work, as I can't figure out how to pass those secrets from my workflow yaml file to my root level config.yml file. Any help would be greatly appreciated!