I do this every time before I upgrade to a new iPhone.
Connect your iPhone to iTunes and from the main menu, first choose to Transfer your purchases to iTunes, to get any apps that you've bought using your iPhone into iTunes for a record of the most current activity. After that process is finished, right click on the dropdown arrow to the right of the device name, then choose Backup from the resulting menu. Wait a little while for it to finish.
Next, I plug my new empty iPhone into iTunes & choose Restore from Backup. The result is essentially a clone of my previous iPhone. Everything transfers: music, documents, all apps, Settings, text messages, photos, video, ebooks. Everything. This is my third upgraded iPhone & it worked like a charm each time.