How can I update existing config from a custom module's config/install yamls? I added some config yml files to my module's config/install directory so that it is installed directly when installing my module, it works well only if there isn't a config file with the same name installed already and only if it's the first install.
  So my question is there a way to update the config files already installed with my module's config file, and delete them when uninstalling the module ?
A module install should not update config. If you want to update existing config, your module should implement hook_update_N() (see docs) instead.

However, you could add a dependencies: enforced section to your YML config files. This will remove your existing config on module uninstall, and install the newest config on module reinstall. This way you can "emulate" a simple update mechanism for your own, private custom module. See doc for enforced config dependencies