The drush directory is intended to contain drush configuration that is not site or environment specific.
Site specific drush configuration lives in drush/sites/[site-name].
It's recommended to install Drush aliases in your repository that all developers can use to access your remote sites (i.e. drush @mysite.dev uli).
You can download aliases for Acquia Cloud sites by logging into https://accounts.acquia.com and going to the Credentials tab on your user profile. Download and place the relevant alias file into drush/sites.
You can also generate aliases using blt recipes:aliases:init:acquia to generate your aliases and place them in the drush/sites directory.
Warning this is a destructive operation and will wipe all existing aliases in the file named .yml. You should carefully review the output of this recipe prior to committing (to ensure that local aliases or other manual customizations are not lost).