I'm not sure I'm following you.
In general I have work locations defined by subfixtures that mount to an overall fixture plate that is bolted to my table. I use different offsets (under setup offsets) to define new coordinate systems (offsets from home) for the subfixtures to match where my part is located in cad/cam. Used like this I home, I check some reference locations on my main fixture plate with an edgefinder, then use the appropriate work offset for what I'm going to machine. I rarely rehome/zero (like months...) and keep the machine powered on. If I'm going off fixture I just set zero with an edgefinder etc. I only touchoff if I'm changing a tool or Z datum.
Hopefully I'm making sense. The controller doesn't care if you zero, it'll just use whatever you've got set. You just need to make sure that works for your stock and how you've done your cam.