I would've thought it would just overwrite the '05 apps.
Start up iPhoto go to Help> About iPhoto.
If it says that its version 6 and you can't see any other iPhoto applications in your Applications folder then its a fair bet that its been overwritten and all is well.
If not, just drag and drop the iPhoto 5, iTunes 5, iMovie 5 applications into the trash and import your files into the '06 applications when they start up.
Hope that helps