Hey guys, I'm about to complete my PhD thesis, but I'm unsure of the best way to write my acknowledgement section as my situation is quite complicated:

My original principal supervisor left the university (but he is still listed as an external co-supervisor), so my co-supervisor became my principal supervisor for a while before the university said she can no-longer be my principal supervisor due to some university rules and policies, so she became my co-supervisor again. Then I had another principal supervisor (current) assigned (who had been my other co-supervisor since the first principal supervisor left the uni).

What's the best way to acknowledge them in my thesis?

Hehe, sounds confusing! Mine was a bit similar! I had stopped working with one supervisor and had a new primary supervisor assigned and all sorts of confusion as well. I just acknowledged them all in what seemed like the best order. No point in accidentally offending somebody. They probably all did give at least a tiny bit of input at some stage. If not sure of what order to put them in, maybe base it on the order they would be listed as authors if you were to publish a paper from your thesis and they were all to be named on it. Hope that helps.

I had something similar also. I basically listed all supervisors and noted which years they were involved and also, for one of them, which particular area of my thesis they oversaw. i.e.

Prof X was the Principal Sup of this thesis from 2012 - 2014 and provided invaluable guidance in data analysis of Study A. Prof Y was the Principal Sup from 2014-2016 and Prof Z was the Co-Supervisor from 2012-2016.....

Given that I used my acknowledgement section to thank my, now deceased, dog for her loving cuddles and big sloppy licks during the "dark times", I am probably not best placed to offer advice.

Yep, I really did write that. She really did do that for me. And yes, my descendents are going to be reading that section and smiling for generations to come.
I wanted to insert a colour photo of us hugging but my supervisor said "best not" and the discussion ended. :-D

As long as you mentioned your supervisors' names before your dog's... :D

I don't think there's anything wrong with mentioning your dog's name before your supervisor's, if the dog has been more helpful than the supervisor.

Haha, very good!