You really should get into the habit of always zeroing anytime you start a new job and certainly anytime you change bits. The only exception is if you have an automatic tool changer, in which case the machine zeros for you.
It's really simple to zero to the top of material. I never use the plate method. That's too cumbersome and often leads to chaos (forget the clip ever?). Instead, I have a bright light mounted on a wall near the machine and use the light to determine when I've lowered the bit to the material. I use the "K" to get it close, then "D" of .01 to bring it the rest of the way. Been doing that for years and have never lost a clip! The only time I have trouble using this method is with clear plastic. In that case, I put a sticky note on the material and zero to that.
You can zero to the spoil board, no problem. Where you zero is controlled by the program that generates the toolpath. I virtually always zero from the material. That way, I never get confused as to which method I'm using. Start mixing them up and you'll end up with a large gouge in your spoil board and probably a broken bit or two as well.
ShopBot Details:
2013 PRS 96x60x12 (Centroid upgrade)
4hp Spindle
12" indexer
Aspire
Rhino
Fusion 360
Ferrari 360
Prusa MK3S+
Prusa XL multi-tool