it is possible to use a, for example, amp or FX in iPad (with the iDevice cable) and send it over the OUTPUT to a PA system without afecting the guitar?. I mean the iPad app should not affect the body of the guitar.
It will automatically do that when connected to the Output jack.
You can specify whether or not the iDevice effects are passed through the TWA EFX or not also in the Insert menu.
Sometimes I'll mute my preamp and use only the Midi effects from Sampletank with no effects from the TWA.
It works all sorts of ways. :)