I've just bought a Sonic Pro Vx and I'm brand new to recording music, so thank you for posting the solution to ensuring Mobile Pod recognises the guitar input! I was convinced I was doing something wrong til I found your posts as I had the mic turned off in the ipad privacy settings.
Nizzag and McKens, I was searching last night about how to link MobilePod and GarageBand and I found this useful Youtube link.
I only got to test the solution very briefly, but it seemed to work for me.
Hope it helps.