I would go with the setup you are currently using. Which version of software is on his 5504? You can check it by pressing 411 then Replay Zones. The number should have 190 at the end, that version fixes that Channel 6 problem.
Anyhow, if you are using the IR Blaster to change channels on the DirecTV receiver, using the internal tuner for locals on the ReplayTV is more reliable. Also, the setup is more direct by using the Replay's tuner. Finally, if he uses the internal tuner on the Replay and the Antenna output to the TV, it's easier to record one thing while watching something else live.
Anyhow, if you are using the IR Blaster to change channels on the DirecTV receiver, using the internal tuner for locals on the ReplayTV is more reliable. Also, the setup is more direct by using the Replay's tuner. Finally, if he uses the internal tuner on the Replay and the Antenna output to the TV, it's easier to record one thing while watching something else live.