First of all you need to stop itunes automatically syncing your iphone.
Go to Edit, Preferences, and the Devices tab. Check the option "Disable automatic syncing for iPhones and iPods".
***BEFORE you plug in your iPod,
Then connect your iphone,right click the iPhone icon in the left-hand list of the iTunes window, then transfer purchases.As long as your PC is authorized that should do the trick, for your apps.
I use this for my music:click here