Sync Apps between iPhone and ITunes before install of IOS6?

I use an IPhone 4. I always purchase my apps directly from the IPhone, and never from my computer.
The consequence is that there is no sync whatsoever between the actual screens/folders/apps on the IPhone and what is displayed on ITunes, in the TAB "apps".
Last year, when I installed IOS 5, I killed all my apps on the IPhone, and it took weeks to re-install my apps and the folders.
I am not prepared to suffer this exercise again, and I am even considering to skip the install of IOS 6 to avoid this pain.
How can I mirror the content of my IPhone such that the apps and the folders content/position actually present in the phone are memorized in  Itunes?
Your help would be much appreciated.
Patrick

I figured out to click on the "transfer purchases" to get my apps synced.
Now I have a new question.  How do I delete apps from the list that I do NOT want to install? 
Thanks. 

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