How can I keep from losing apps, data and photos with iTunes?

I am setting up an iPhone for the first time on iTunes.  I am trying to prepare for moving to the iCloud from me.com.
- I authorized the computer running iTunes>>>  successful, I think
- transferred purchases to iTunes>>> successful, I think
- I synced the apps >>>  all apps on the iPhone were deleted
- went back to sync apps & selected the boxes in the left panel>>>>> apps were installed on iPhone, no organization, data lost
- restored iPhone from (automatic) backup>>> all apps were restored with data & organization, then iTunes automatically synced & removed apps
- selected sync apps to be able to select all apps in left pane, but did not apply sync
- restored iPhone from (automatic) backup>>> all were restored, but iTunes has not yet synced to remove all apps
How in the world do you get iTunes to save the apps & data that you have without having what you have wiped out?
I don't have anything but the following:
- apps + data
- contacts
- email
- calendar
- photos
I have no songs, videos or other media.  I have only what is on the iPhone.  I am NOT trying to wipe it out or put info on it from my computer. I just want to upgrade the iPhone to the latest iOS and preserve what I have on the iPhone.  Is this an unusual expectation?  Why does iTunes wipe the iPhone when it syncs?  Shouldn't I have to somehow delete something without it automatically being deleted?
It is like having a living, breathing NIGHTMARE!
Can someone please advise me the steps to take to do this?
I am just trying to prepare my wife's phone so that I can try to move both our phones to iCloud since me.com is disappearing.  I can't wait to start the process of actually moving the phones.  What will that be like if I can't even get her phone upgraded to iOS 5.1 without losing everything?
Please help.
Thanks.

I forgot to mention that I am running iTunes on a Windows 7 PC.
I put this in a reply because I couldn't find out how to edit the post.

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