Re: What 'app' is he using ?
The mini has a 1/8" line-in, for the large one (Kaoss Pad 3 at least) you need to convert to RCA plugs. I did have a Kaoss Pad 3 for a little bit that I used for Synths and for guitar, in the end I figured looping was easier with a real looping pedal and while the filters and stutters are cool, I figured I wouldn't use them long term.
As far as the app, something like the iRig should work.
(EDIT: I didn't watch the video, just commented based in Kaoss Pad content)
I just watched it, I agree with Alpaca's post. It's some sort of synth app (could be Korg) being played next to the pickup.