This seems like a tricky proposition but maybe I am overthinking it.
We have a 4.1 cluster with 4 virtual hosts. We have a new 5.5 cluster with 7 new hosts. The new environment is completely built and we have been upgrading virtual machines from our 4.1 environment by moving them in to the 5.5 environment and using update manager to perform orchestrated virtual machine/vmtools upgrades. Everything is working quite nicely.
Our vCenter 5.5 VM up until this point has been running as a virtual machine on our 4.1 cluster. We did this because we wanted to virtualize it but wanted to put it in (At the time) a running production environment, which was our 4.1 environment.
My question is, when it is time to upgrade the vCenter 5.5 VM, I need to migrate it over to my ESXi 5.5 cluster. Then, if I follow the same procedure I have been following, I will initiate an orchestrated upgrade from the vSphere client/web interface on the virtual machine. At this point, the VM is going to be intermittently unavailable while it upgrades, so I won't be able to use vCenter. That is assuming this method would even work, because update manager runs from vCenter and vCenter won't be up. And what if it fails? What the heck do I do then? 
So, what method do I need to follow to do this?