Software Deployment

Hi there, I repackage an application and there is SideBySide in the normal %SystemRoot%\WinSxS folder. But the application also made the folder
INSTALLDIR\Microsoft.VC80.ATL
with the files:
Microsoft.VC80.ATL.manifest
atl80.dll

And in the CommonFilesFolder there is also the folder
INSTALLDIR2\Microsoft.VC80.ATL
with the same files (same version, same text).
Why is it also in the INSTALLDIR and not only within the WinSxS-folder? What's the sense of this?
By the way: I deleted the files and folders from the INSTALLDIR and the application still runs.