In an existing Drupal site, execute drush make-generate drupal.make
Create a new Aquifer project.
Copy in that makefile.
At this point, you’ll need to bring in your custom code into the Aquifer directory structure
From there, aquifer build should generate a build directory that looks just like your existing docroot. After testing it thoroughly, you can use Aquifer Git to deploy your project to the existing repo for deployment.