I've split the cases both ways and I have to say, if you are just working on the bottom end, turning the case upside down is the easiest. A little trick is to tightly zip tie each end of the crank up and around the same side spark plug first, before splitting the cases. This will keep the crank in the cylinders nice and tight so you don't have to worry about it coming out.
When you put it back together just set the tranny in the lower case, pick up the upper case, which will have the cylinder and crank secured and set in down in the lower case. This way you don't have to worry about lining up the tranny and shift forks. Real easy to do.