Generally one of the two sides with the nodes(alternating node pattern)will be the stiff side...but not always. I place the node side against the bow and the stiffer side of the two is preferred(for me at least). If it doesn't fly well that way, flip it over and try. Generally that will solve that problem. I also generally cut the nocks just above a node and wrap with sinew(or thread set in glue) but it is not necessary to cut above the node as long as you wrap below the nock.
With cane shafts, as well as hardwood shoots, it is not critical to get the shaft completely straight. Obviously the straighter the better but if the point and nock ends line up and the arrow spins true it will fly well. Cane arrows are very tollerent of different draw weights. I like to leave the cane(and hardwood shoot)shafts a bit longer than with store bought shafts. The natural taper of the cane(and hardwood shoot) will reduce the effective spine weight by about 10# to 15# so a 60# spined cane arrow will generally shoot well from a bow of 45# to 70#. Any length over 28" you can also reduce the effective spine weight by 5# per inch.