When measuring horses that are asymmetric through the whither with my EFS horse measuring system, I suggest that you pad up the small size until both are equal, then measure over the shims. I have also measured the large side and used the resulting measurements on both sides to build a symmetrical tree. Either way, we always build the tree symmetrically, and when you get the finished saddle, you will need to shim the tree to level it.  The asymmetry usually comes with a rotation, the cable rigging position can be altered with a strap on one side to help keep the saddle from falling over to the small side.