Welcome to the discussions,
After you set up your new phone, iTunes will ask you if you want to set it up "as new iphone" or restore it from an existing backup, which in your case would be the latest 3GS backup. So you can use this backup to restore all compatible settings and data to your new phone. See what's inside a backup here:
http://support.apple.com/kb/HT1766
You can use more than one device in iTunes with the same account, and iTunes will remember the settings for each of those. Applications can also be used on more than one devices, but you'll have to use the same iTunes account.