Overview & help with drupal files and folders on Win 7
The confusion is probably resulting from things that differ from the Windows environment compared against the traditional multi-user LAMP environment that Drupal is usually built against.

To explain what those directories are in the order you listed them:


The DevDesktop application code
Your sites you're managing with Acquia
Acquia application configurations
Drush application configurations


This data is separated mostly to accommodate a multi-user environment. So that...


All the data for the DevDesktop application is isolated so multiple users can use the app.
The sites you manage are separate from other users.
Your Acquia application configurations are separate from other users (e.g. your login info).
You Drush application configuration is separate from other users (e.g. your site aliases).