well the best person to answer that stuff is DrLava and James.
basically i like to start by measuring one channel at a time and tuning the bias to 0v and the gain to a 5v swing on each
if there is clipping in X and Y you will see flat spots at the top or bottom of your wave form
the top wave in this pic is not clipping the bottom one is clipping VERY BADLY.
this is what digital clipping looks like.
Once thats all looking good, throw the scope in XY mode and play some test patterns.
for X and Y make sure scope is set to DC or else it will try to center everything