The deal is, as far as I understood from my IR examiner, that they can test you on any and all functions and equipment fitted to the aircraft. So a thorough knowledge of the G1000 is essential.
They will tell you when you can and can't use certain of the tools, for example my examiner asked me to switch the MFD away from the map display during the NDB procedure. You are expected (or at least we were) to enter the FP on the G1000, and I can't see them not allowing that, though they can fail anything that can safely be failed at any time, so make sure you keep on top of your situational awareness.
I reckon the DA42 is an extremely good aircraft to do the IR in. The most important thing is to have a very thorough understanding of the massive functionality of the G1000, it's not for no reason that they fit them to bizjets and the like!