Help migrating to a new iTunes

Hello,
I recently got a new mac and I'm having a trouble syncing my iPhone with regards to Apps.

I want to sync my Apps to my new iTunes while keeping my Apps-folder-structure exactly the was it's on my iPhone. While I did transfer all my purchases, including music, to the new computer, doing the same for my Apps has proven a difficult task. Whenever I was to sync my apps, iTunes shows me all me iPhone apps but not in their Folders, i.e. I would have to waste more time setting the apps exactly the was I want it to be
How can I fix that?

Note: I have successfully transfer all my music and the only thing that bugs me is the fact that I will need to organize all my apps on my iPhone (it will take a long time), if I do sync it. I do have all the files on my other pc computer, thus I can transfer any configuration file necessary to the new mac, if it will help.

Thanks

If you transferred your iTunes library in it's entirety to your new Mac the phone layout, apps etc would be there.

Do you still have access to your old Mac to re-do the transfer? Because it sounds like you may have missed some parts.

Hey,
It's actually a PC and I have transfer the ipa files so I'm not missing any app. It's the way all my apps are organized on my iPhone that will be gone, if I'll sync.
The problem lies in the fact that I would have to work hard to reorganize apps and my folders. It's too much work.
So the question is, is there a configuration file I can transfer from my pc to my mac that will enable me to sync my apps so the Folder Structure on my iPhone remains after the sync?

Note that I have transfer my purchases from my iPhone. It doesn't solve the problem

Mac or PC, doesn't matter the transfer process is the same.

You move the whole folder and the two library files.

The ipa files are, as you say, just the apps.

If you look here:
iTunes: How to move your music to a new computer

Particularly the External drive part and make sure you have transferred all appropriate files. I suspect it's the library files that are the issue here