I suspect everyone already knew this information but it took me a while to get it straight in my head and working the way I thought it should.
If I still don't have it right please feel free to correct me, or add more information.
Mach3:
Safe Z settings in Mach3 seem to have to do with protecting the machine and bit. It doesn't seem to be connected with anything set in VCarve Pro contrary to what I was trying to will it to do with my mind... Yelling also has no effect it seems.
Config->Safe_Z Settings
In here you can pick Machine Coordinates, Work Coordinates, or Incremental.
This is used when you hit Stop, or if you stop the job and hit Run From Here. When you hit RFH, it will ask you to "Position" itself, start the spindle, and then go to where it left off.
I set this to Machine Coordinates, and picked a high enough point to clear anything I might have ( Negative Number for me ).
I ran into an issue where I hit RFH and managed to put a nice cut right across the piece I was working on because SafeZ was not set. ( "I TOLD YOU NOT TO DO THAT", had zero effect )
2010 Screenset in Mach3:
Offsets-> Use Safe Z
Mach3 Safe Z Settings must be set up first before you can enable this checkbox.
VCarve Pro:
These Safe Z settings seem to have to do more with moving the Z axis during a cut and making sure the bit clears things that might be in the way ( fixtures, clamps, etc ). It has no effect when you hit stop and/or Run From Here.
Under Material Setup, there are settings for Clearance ( Z1 ) and Plunge ( Z2 ).
These are Above the material ( assuming your 0,0,0 is on the top of the material ).
Every time the tool needs to change position, without cutting, it will raise up to Z1, move, and then rapid down Z2, and then slow down to plunge.
These settings are per job.
I set these to make sure I clear any clamps, etc when moving. A lot of time I use the old tape and glue hold downs so I can leave Z1 pretty low, and Z2 close to Z1. I had it much higher and was wasting a lot of time moving.
I spent some time testing these and they appear to be working for me now, finally.