So the process in the manual (work off the material top) never sat right with me. And I saw the older forum post where someone made custom M Codes to zero out more like a different control. However talking to a couple guys at work today they showed me a 3rd option.
Using the tool setup menu under run and a tool setter on the table or vise ways (whatever you can reach) Go through the process of selecting each tool and wheeling down and zero out each tool (They use cheap $60 ones at work and they seem to work fine for non .0001" critical applications).
From there you can then G54 (or other) your coordinates as normal and use the tool setter to set your G54 Z wherever your CAM is setup.
Just ran through it and it worked great. Couldn't tell the difference between the part I ran last night and the one I ran today using the process in the manual and this new tool offset setup.
I figured I would share because I thought I was resigned to setting tools each program and hopefully someone else thinking the same thing will now run into this.