I've really started getting into Podcasts, but I hate how they can mess up your iTunes library organization. And iPod synchronization should be hassle-free, given they're called Podcasts.
So here's what I do with iPodderX and my iPod. I set all the feeds I want to sync with my iPod to be saved in a playlist named "Podcasts." To set the playlist location, double click on the feed name and type in the name of your playlist.
Then I make a SPL from the Podcasts playlist and limit to new podcasts within the past four days. I suppose you could use other limiting factors like time and space, but this works for me.