iTunes although does a great job backing up all the data which you can restore at any time if you have issues but if you are upgrading hardware, i.e. 3G to 3GS or a major OS update like version 2.x to 3.x, restoring from old stuff may often create unnecessary legacy files left on the system, slowing up the OS or in some cases may also contribute to battery depletion issues (This has not been confirmed yet but there might be some conflicts in the system that might cause faster depletion of battery).
So the best way to get started with your brand new system would be to connect to iTunes and select “Setup as new” instead of “Restore from backup”. This will ensure that you have a fresh and clean system running without any kind of conflicts going on in the background.
Before you do “Setup as new” phone you will need to backup your important files/data. The process of backing up your data described below is a manual backing up procedure and would require you to have SSH access to your iPhone. If you know what I am talking about go ahead and proceed at your own risk. Backup these following folders so that later you can restore them manually after you have your new System up and running. In most cases it will be a very easy Copy/Paste operation of the following folders after you SSH to your iPhone. Continue reading