Extract the downloaded .zip inside the themes folder. Rename the extracted folder from hugo-whisper-theme-master -> hugo-whisper-theme. You should end up with the following folder structure mynewsite/themes/hugo-whisper-theme
Add example content
Copy the entire contents of the mynewsite/themes/hugo-whisper-theme/exampleSite/ folder to root folder of your Hugo site, ie mynewsite/
To copy the files using terminal, make sure you are still in the projects root, ie the mynewsite folder.
cp -a themes/hugo-whisper-theme/exampleSite/. .
After you copy the config.toml into the root folder of your Hugo site you will need to update the baseURL, themesDir and theme values in mynewsite/config.toml