AutoTune is a plug-in.
It will work with Audition 3 or FL Studio 8 and many other music production software.
It won't be incorporated with a program. Its a plug-in that you load up while running Audition 3 or FL Studio 8.
You then apply it to a track, or effects send track, and work it.
EDIT:
Make sure you have the Autotune .dll file in the VST Plugin Folder. Load up your software and scan for plug-ins.