Have you tried plugging in each device? It should recognize both phones seperately and for each device you can choose what should be synched.
It's the same as if you have an iphone and an ipad.
Just plug them into your pc and open iTunes. You can set them up as completely different devices and files in the iTunes settings. Here is a guide by Apple on how to do it. My wife has an iPhone 6 and I have a 7 Plus. We both use the same Apple ID ( you can use separate Apple ID's if you so choose ), but have completley different apps and settings on our phones. Works awesome in iTunes. Just use the guide I linked.