There is a power switch on the controller and one on the spindle.
At the end of the day, do I need to shut both of these off? and at the beginning of the day do I need to re-initialize anything or does the machine save the set-up file?
or can I just hit the power pendant off and walk away?
Best to power down. If you get a lot of lightning in your area unplug vfd. Vfd’s are expensive to replace. The SO5 had a warm up cycle for spindle before use. That gets bearings lubed up inside.
I have multiple machines with VFDs, none have been intentionally powered down in the last 12 years or so-- lots of power outages, so they do get power cycled every month or two. No issues so far, but YMMV. None of these are inexpensive no-name VFDs, so that might make a difference. (I haven’t looked to see what’s inside the Shapeoko box, I have to admit). Having to turn them on and off every day would make me a little batty as I’d invariably forget and then spend time cursing about my machine not starting before remembering to turn the power supply on 
i always power off the machine & i always forget to power off the VFD…well my box just stopped working. carbide sent me a new piece to fix the spindle power box & it worked, but i will be powering it off from now on. Also, yes you have to initialize every time you turn the machine on, but it does save your last Zero and your set-up file.
When done for the day both get powered off, power up the next day and reinitialize. If storms are expected they both get unplugged.
I power mine down but the switch for the VFD is in an inconvenient location. I simply trip the breaker which is much easier to get to.
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