The simplest way is to just make all of the cords the same length and all of the weights the same length. 
The difficult way is to make one cord longer and put a slightly lighter weight on it, this takes more skill though as the reason you have to put a lighter weight on it is because the longer cord makes more centrifugal force, (correct me if I'm technically floundering here,) making the weight pull more than the other two weights with shorter cords so you need a lighter weight to make it pull the same as the other two shorter corded weights.  So it takes a little experimenting or just to get that right, or just a proper math formula I guess.  The way to get that right would be just to braid the rope a length, tie on the weight temporarily and try a throw, if they open up nicely like a helicopters blades then it is good if not shorten or lengthen it as needed and tie on the weight again.
  But I recommend the 3 weights of equal weight and cord length, it's what I made after I researched this.  I made mine by carving wooden balls out of a yellow birch log and made them a little smaller than tennis balls but they could certainly be bigger.  I braided the cords from jute twine then drilled a hole through the balls and rounded off the edges of the hole so it wouldn't wear too bad on the cords, then I made a knot in each cord, round braided a length of the cord to go through the ball, (not necessary,) and then pushed it through and tied a knot on the other side.
    Here's some good plans on how to make another type of wooden bola and how to make a stone bola, they probably work great too as paleo knows his stuff, I used the braiding instructions he gave by the way, worked great.  http://paleoplanet69529.yuku.com/topic/36831
  This is the wrong topic section too.