Like I said, it is idiot proof. You did what you needed to do, transcode the video into MPEG-4. Now just add the video to iTunes (I'm pretty sure that is all you have to do). I don't have a Video iPod myself, so I don't really use iTunes that much (for my regular iPod, I use Winamp). I'm sure if you just drag the video into iTunes though, it will recognize it and add it to your iPod.

Hopefully my information is "idiot proof."