Your work flow is not correct for operation on current TiVo systems.
If you are on TE4 software then press the right arrow on the circle pad at top of the remote. That brings up the current programs on the various tuners. Scroll up/down to see the programs you can select from and change between them as desired.
Obviously add a "Pause" button press before changing between tuners if that is important to your needs but keep in mind there's only so much buffer to work with.
I can't say for sure that you can Pause on a tuner and then flip to another tuner and pause there without affecting the Pause that was happening on the original tuner. Test that first before assuming.
With the workflow you are using you lose the buffer as soon as you change the channel. You aren't pausing, you are literally (from your description) changing the channel. Changing the channels flushes the buffer and starts it over again with the new channel content.
Using the Right arrow on the circle pad changes the tuners. The original tuner continues to capture the content you were watching. You could go back to it and scroll back if desired (in case you missed something while checking out the second tuner's content). That is what I think you are trying to accomplish.
Oh, when you have the list of tuner content up and you want to go back to just watching what is on, press the Left arrow on the circle pad. Changing between tuners is done by selecting a different tuner's content and pressing the OK button (middle of the circle pad) when highlighting the content you want to see.