Yea, using transpose after starting with Thunder I/II doesn't do anything. It only works with Astral Fire and Umbral ICe stacks.
My basic single rotation Thunder II > Fire I until mp is low > trasnpose > bliz I repeat at low levels your mp should be back up to full after bliz I. For higher levels it gets a bit trickier, when you add in Fire Proc and thundercloud. And you will have fire III and bliz III
for multiples, basically the same, just replace fire I with fire II. Although watch out as this will eat MP faster.