I have a similar situation. Setting the gains with the CD means that when I use my 4g iPod nano through the full speed iPod cable connected to my Alpine 9887r the bass is noticeably quieter. If you reset the gains using the DD1 tones on the iPod the gains will go up before showing distortion, for this I downloaded the tones off the D'Amore and put them on my iPod.
Link to the test tones as found on the D'Amore site
https://files.secureserver.net/1sQHliMu6YbY7V
Of course you will only be setting the gains for use with the iPod, there is no guarantee that what you play through the CD player will be "clean" of any distortion.