I have two TiVo V6 boxes in separate rooms. I also have a Harmony Hub that sits in one room with an IR blaster going to the other.
I added the TiVo V6 box to the Harmony Hub but if I use the Harmony Hub to for example change a channel it of course changes both channels.
I have found that other models of TiVos allow you to change the infrared channel on each box and manually set each up on the Harmony Hub.
The process involves holding either the TiVo button + pause or TiVo button + green button for 5 seconds. Pressing a digit for the channel you want to set the box to and then any button to send the channel to the box.
Neither of these methods work on a V6. However I suspect it's possible because in Device Information it does list the Remote Address as 0 which is the expected default.
Hi: I just found your post about separately controlling two V6 boxes. I am in a similar position - though one is a Tivo and the other a V6. As you state if I try control one box it affects the other. Because of the location of the boxes using IR is the preferred option. Or did you go down the suggested one IR one RF / both RF route?