There is no way to automate different file types going to different places. You set a default location and, based on whether you have the organize/copy boxes ticked, stuff downloaded and added to iTunes will go to one place, but you'll have to manually change the location of stuff on your own. Anything downloaded from the iTunes store goes to the iTunes music/media folder by default.
The easiest way to do this would be to set the iTunes music folder to the internal, consolidate all of your audio to it, then untick the "copy files" box in iTunes preferences and manually manage your video files.