>When upgrading the stack does the entire stack upgrade at the same time
Correct. And reboots at the same time.
I don't work with Hyper-V in particular, but a low cost solution I have used before is to add in a third low cost "heartbeat" switch. Typically you just use a Gigabit copper port built into the server and plug it into a Gigabit port on the third switch.
Then when the main stack reboots the nodes don't go spastic.
Another option is to not stack the switches - but you loose the ability to channel across the switches. If you are using Hyper-V then this may not be an issue.
I guess another expensive option is to use a pair of stacks and dual connect the servers across them.