So let me understand , you have an old TIVO and a V6 box currently. You have received 2 mini boxes.
Firstly, the old TiVo has all content going via the coax including it's on demand content whilst the V6 needs internet access via ethernet or Wifi to access the on demand content with the coax used for live tv only.
So if you leave your v6 as is and not swap it out with the TIVO , is there no upgrade option as it is surely connected to your internet currently either via ethernet or wifi.
In answer to your question of why 2 minis , there are a possible 2 reasons for this;
1 it should have been 1 main and 1 mini to fully replace both your existing boxes
2 you have been sent an extra mini in error and should have been sent 1 mini to replace your TIVO and you upgrade the existing V6 box.
In either case did you get 2 new tv360 remotes.
In my case when I upgraded, I got 2 new remotes only and my menu enabled me to upgrade my 2 existing v6 boxes over the internet.
Equipment;
HUB4
x2 V6 Upgraded to tv360
Ultimate Ooomph Gig1
Wifi Plus
VM Telly Tablet