tt2--
At the risk of appearing overly dense, I think I did as you suggest with less than great results.
I first edited Preferences as you suggested.
I then synced the iPod as usual (On my Device/Podcast/Edit...right clicking yesterday's partially played podcasts and podcasts that are now dated marking them as played), then clicked Refresh and then synced.
After which I selected the phone. I had two options (I think)--right click the podcast name and mark as played or uncheck the episode(s), Done, Sync. I first chose to uncheck the episodes which didn't work well for two reasons. One of the podcasts consists of 3 episodes/day. However, despite the 3 being unchecked, the 3rd hour (3 of 3) still syncs. Also, since I normally sync the iPod first in the morning it makes more sense to just mark any podcasts that I do not want to sync to the phone as played instead of unchecking the box.
I still, on the phone, had to manually delete episodes that the phone had downloaded on its own when not connected to iTunes (I changed the setting on the phone to not allow podcasts to download on their own when unattached to iTunes). I had thought that a sync from iTunes would have superseded the target device and removed any podcasts not a part of the set being synced--but it did not.
This all said, it's not what I had hoped to be the solution. Frankly, iTunes allowing for separate, local device 'accounts' with each device having it's own sync settings for podcasts (or whatever) would be far simpler and more time economical.
Mark