Not exactly. You may have misunderstood me.
I really do have a Cablevision box connected to the RF input, and those channels get mapped as the 1002-1099 Replay channels. The Dish channels get mapped as the 2-999 Replay channels. What I'm saying is the when I change to channel 2 on the Replay it changes to 2-01 on my Dish 6000, and when I change to channel 5 it goes to channel 5-01, and channel 9 goes to 5-02 on the 6000.
I believe what happens is that when I change to channel 2 on the Replay it sends a 002 (not just 2) to the 6000 and it knows it's supposed to go to 2-01, and when I change to channel 9 on the Replay it sends 009 (not just 9), and again the 6000 knows it's mapped to 5-02.
I suggest you check what your 6000 does when it receives a 002 or 009 compared to just 2 or 9. (change the channel examples to whatever your OTA channels are in your 6000 setup, the examples I give are for the NY area).
Here's some additional info on my setup.
the Replay Dish code I use is 9775.
Replay model is 3060 (upgraded to 120GB).
Dish 6000 software version 777PCNDD-N.
Hope this helps.