I don't understand how to link the higher level controller of a WIP

Hi! I am trying to simulate a wheeled inverted pendulum with a partial feedback linearization law. I would like to control its velocity with alpha and theta. The problem is that there is a lower and a higher level controller and I don't understand how to link them. I did this scheme and it works if I set a constant alpha_ref, but I have to change it because I have this control law for the alpha_ref dynamics: with vd the desired velocity. Any ideas of what I should do? I attached the article I am following If someone would like to read it. Maybe it's not the right place to publish this post, sorry for that.