The Remote is RF so they would be paired to the specific box and not need line of sight as IR does. The remote light would blink in yellow.
When the remote is in IR, then the remote light is red and it can control both if the Tivo is set for IR address of 0 (zero).
Holding Tivo + C switches to IR mode.
Holding Tivo + D switches to RF mode.
To set the IR address, you would need to switch the remote to IR mode, then Hold Tivo + Pause until light blinks, then press a number from 1-9. The remote is set, but the Tivo box is not but it would still respond. That is when you have several Tivo boxes, all would respond since they are still on address zero. To set them, cover the other Tivo boxes so they won't respond to the IR. use the respective remote you want to control the right Tivo box and go to the Settings menu/ help / System Information and leave with the left arrow key. That box is now set. Repeat with other boxes with their remotes.
After that, you can return to RF mode, if you prefer.