So here is the trick: you need MIDI bridge app which allows you to make complex midi routing.
And here are screenshots on how it should be set up:
Couple of days ago I posted overview on iPad DAWs (I've covered Auria, Beatmaker 2, Cubasis, FL Studio, NanoStudio and Tabletop) - http://www.ipadmusic.com/daws-for-ipad
It would be nice to hear what iOS DAW do you prefer and why.
I always were thinking about iPad DAW's as closed apps, you just choose one and make track or at least part of the track in that DAW.
But with virtual MIDI things are changing and even Garage Band doesn't look so closed to external world.
I like how Garage Band instruments sounds but I never finished track there. I don't like FL Studio user interface but they have nice instruments. And I found Cubasis fantastic for composing and arrangement.
So what if we can take advantage of all these apps combining them together... see the video:
Today KORG updated their apps to support Virtual MIDI and Audiobus. So now we can use our favorite DAWs - Cubasis or BeatMaker (they both support midi out and audio tracks) with KORG apps. And thanks to the Audiobus we can record in audio what we play in iPolysix (you can do the same with iMS-20 or any other synths that support MIDI and Audiobus). I recorded video showing how it's all work together. Try it the same on your iPad!