sync app -> icon rearranging

Hi to all,

I reinitialized my imac and reinstalled macosx, I connect my iphone (containing all the apps within their folders and settings) and I transferred bought app, now the apps are in itunes too, but if I go into the tab app of the iphone (always itunes), there is no check on sync app, if I put the check it tell me that the app of the library of the computer will overwrite the app on the iphone and if I accept I see all the app rearranged out of the folders!

I don't want to loose all my folders and settings but I need to put the check on sync app of itunes to synchronize the app in the future

How can it be solved???