Sometimes I'll turn down the Rig or Cab volume to even things out, not sure if that's the right answer but it will work. Seems over time I've increased the volume on all my rigs from where they originally were, too much of a pain to go back and adjust them all.
Stupid question - was the volume on the iPad cranked up?
The AUX In will accept Live Level signals- if you were using the headphone out from the iPod, you were likely sending a much lower level signal.
You can connect an inexpensive audio interface to the Lightning/previous connector that will send a Line Level signal to the KPA.
You could put a pure boost stomp in the x stomp space and lock it, if you're not using that for any of the rigs. Just use it to cut instead. That way you won't have to tweak each rig separately.
Mod?
Are you the edge?
Sorry, my wink emoticon didn't work.
...)