Two Questions

I just got a new iPhone4 in warranty.

1. For future reference, is there a way to save on iTunes the way i have put my apps in folders? When I synced the new phone, all apps there but most were not put in the folders I had them in.

2, Is there a way to save the wifi passwords that I have logged in location by location?

 

Everytime I sync my phone, it says "backing up" first. So I assume you are saying I already backed up my old phone.

I have not done the right click, restore as you said but I'm confused about the fact that when I sync'd the new phone, I got many of the folders but only about half. Are you saying if I follow the steps above, I will get the rest?