How can i adopt the iPhone App-Structure to iTunes for Sync?

Hello Community!
I usually buy apps or games directly over the iPhone-App-Store and i also manage the folder structure directly on the iPhone Screen.
Yesterday i bought a new App via the iTunes Store on my MacBook (don't know why, i thought it would be no problem)
ITunes is set to manual organisation (the box "App Sync" is not set in iTunes).
So my problem is:
I cannot install my recently bought app on my phone without enable synchronisation with iTunes.
But if i set iTunes to app sync it is going to destroy my folder structures and remove apps i bought with the iPhone EVEN if i click "Transfer Purchases"!
Is there a way to manually install the app without destroying my complete structure and losing apps?
Sorry for the critics, but this is not very user-friendly!
Thanks for Help!
Greetings from Germany ,
Patrick

This article will tell you where your iPhone backup is stored on your computer:
http://support.apple.com/kb/ht4946 iTunes content is NOT part of the iPhone backup. You can either copy your iTunes library to your new computer, or you can re-download your purchased iTunes content(except ringtones) to your new computer; http://support.apple.com/kb/ht4527

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How can i adopt the iPhone App-Structure to iTunes for Sync?

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