Multiple iPhones devices synced to the same iTunes, how to keep podcasts straight?
Have you considered using Downcast, or the Podcaster on your device instead of using itunes for podcast management?  By using an application each device will store their settings separately.  This does have the downside that podcasts that you both listen to, would be downloaded twice.  I long ago gave up on using iTunes for podcast management, Downcast is a far better tool, in my opinion.