Xbsu, you will not lose any functionality of the head unit. when playing actual cds, flip the switch for cd input and the audio from the cd will come through.. when using the aux in, flip the switch and though the cd will still be "playing", the audio from the aux will be coming through.
technically, you *could* just wire in a 3.5mm stereo male plug as your "input" and plug it directly into an ipod, zune, walkman, whatever. otherwise, I'd recommend wiring in a 3.5mm stereo female jack, and either use a 3.5mm male-male stereo cable to plug between that and your ipod or, if you're using a drive+play or other adapter that uses RCA L/R, use an RCA L/R > 3.5mm stereo male adapter cable (avail at radioshack.)
The only real benefit of a blitzsafe universal ipod adapter is that it charges your ipod while it plays. royce has a drive+play which charges and lets you remote control the ipod, slick.
I have not used an ipod 12v car charger with this system but I foresee possible alternator whine, depending on how the car charger grounds itself.
does this help?
whitman