Hi,
You can upgrade right in your "My Presonus" account. I still have S1/2 and S1/3, on my computer but you don't have to have both... your upgrade will be a complete install that doesn't need any of S1/2 so if you want you can uninstall it before OR after...
Your content should all be stored in stems on your computer, and will import into S1/3 , just make sure the folder is backed up if your going to delete S1/2.