Backup Iphone via ITunes

Hi everybody,
I recently downloaded the new iTunes. It had changed a lot compared to 2 years ago when I started to use it the first time.
Back then when I did the backup, I am able to view the outlook of my iPhone (3GS) homescreen and also all the pages of apps. I can arrange and delete it.
And when I restore with the backup, I get the exact replica of it (meaning all the apps and their location or folders).
With iOS 6 and the new iTunes version, is this still possible? I just did a restore from backup for my sis on her upgrade of iPhone4s to iPhone5. This did not happen and she had to re-download all her apps via iCloud.
Could I have your advise?
Thanks

The same applies.
If all apps that were on the iPhone are not in the iTunes library on the computer, the apps must be re-downloaded by the iPhone.

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