Problem with apps sync (don't want to resinstall what is already installed

Hi, I got a problem: I organized my apps pages and folders directly on my Iphone 4G .
But now I want to sync apps from Itunes cause I updated apps from my PC since I don't have wifi and can't update apps which are more than 20MB on my Iphone.
The problem is that the only way I found to sync these updates is to check the "Sync the apps" but then I have to select all the apps I want again, to reorganize them again, and it says that the actual apps will be replaced by these ones so I am afraid to loose all my saves.
So is there a way to get the sync folder on Itunes to be organized in function of the way I organized things on my Iphone?
Actually if I don't check the "sync apps" checkbox (on top of left window) the apps appear the right way on the right window but as soon as I check the box then it seams that I have to do anything again...-_-
Help please...

No I can sync every apps, it's just that if I check the sync apps check box it's just like I didn't had any installed app before.
I tunes want to replace all the installed apps by the ones on my PC

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