Is there any way to sync whats on your ipad to a iTunes library

[SkyStudio]

I just compiled a new iTunes library from scratch, now when I select sync apps iTunes shows them outside the nicely organized folders I had them in, is there anyway to fix this?, it also happens when you restore to a new device, app scattered outside organized folders and users have to pay yet another price just to organize all their purchased or free apps.

Sent from my iPad2 64GB wifi 3G using iPF