Putting user mapping configs inside your project structure /apps/YOUR_PROJECT/config would make sense as this would ease the effort for deploying these with your code. If you manually put configs from Felix console, they'd be persisted under /apps/system/config
Kunwar is correct . Configuring OSGi Check the "Creating the Configuration in the Repository" section , This section exactly explains you how to work with config nodes. This gives more flexibility in handling your configurations depending on your runmodes.
I would say that you are very late in doing this. But its better to do before your PROD deployment do a thorough testing with in your lower regions before promoting to PROD.
If incase this is first time deployment to PROD , then you should be fine, but if the code is already in PROD and you were directly making changes in the Felix console,. then the changed values normally gets saved under /apps/system/config and .config files and it gets priority over your project level configs .