Yes to be safe filler port is the best, But in my case the filler port wasnt opening my mechanic was reluctant to open it since he thought it was a sensor and he didnt wanted to play with it.
My mechanic filled it like @xulfiqar bhae said, And i mentioned the procedure on Vitz owners thread aswell. Their i also mentioned removing the chamber is not required, because you never remove the entire oil, Most of it is still stuck in the transmision. Thats another reason the entire 4L can of Oil doesnt doesnt goes in full.
You just open the drain nut, and then remove the tube inside, the entire chamber/Pan is drained out. And you can refill after putting the tube back and keep filling unless it starts dropping, After that put the drain nut back, Add a little more and your good to go.