HI Michael,
Thanks for your detailed query .
This is solely upto you if you wish to keep the CS6 and CC together as thats not going to hurt the functionality of the machine . Since the end user will be a part of the Creative Cloud for Teams , this would mean they can use both the CS6 & CC as a part of the subscription . There are some products that are not a part of CC such as Encore and if you wish to use Encore, I would suggest using the CS6 version of Adobe products or Master Collection only.
For the files, the Cs6 files can be opened up in CC version of the products . And also , Acrobat is a part of the CCT and the latest version should be available for you .
Cheers,
Kartikay Sharma