If the series episodes are marked correctly, the PVR will skip duplicates regardless of which channel they are on or what time they are aired. The same is true for shows that exist on the PVR drive, but not shows on the external drive. If the show is being recorded twice, there is an error in the guide info for the show. Duplicate recordings can be skipped and skipped recordings restored by selecting the show in the daily schedule. (Press PVR twice to get to the daily schedule.)
Correct. I find it easier just to go through the guide and create all the new timers first and then matching them up with the old timers. Deleting them all first would be even easier but then I run into issues of missed timers and recordings.