The ATC checks all of the repository objects contained in the elements you selected in the Project Explorer tree. Doing this for a package runs all ATC checks for all of the objects in the package.
The ADT shows you that the checks are running with Running ATC checks progress indicator. After completion of the ATC check run, the new ATC check result (set of all findings) is displayed in the ATC Problems view and added to the developer's Worklist.