Ideally, you want the aircraft to be acting how it would be in flight. So yes, but... feel free to try it first without the engine running if that's easier. It might yield good results.
Should a taildragger's tail be raised to a normal flight attitude?
Re part 2 of answer, I bought a digital level from Sears that worked great for EDC-10A install and for D10A pitch calibration, about $35. For RV-6, just place on canopy rail for zero pitch reference to aicraft pitch axis.
