Run /path/to/setup.swift --local from your new project directory to use your local setup script and template files.
Update the setup.swift script's branch variable to point to your branch instead of master.
Run swift <(curl -sS https://raw.githubusercontent.com/detroit-labs/fastlane-template/{branch-name}/setup.swift) from your new project directory to use your development branch's setup script and template files.
Make sure that you revert the branch back to master before merging your changes into master.