Where should linux cnc tool offsets be stored?

Coming from a background in mostly mazak programming and alittle haas the way linux cnc handles tool offsets has been confusing me and maybe it's because I'm not setup with somthing like the carousel macros.

I am currently using axis since it's the only thing that supports the weird display size I accidentally went with. So anyways when I set tool height it moves g54s z value to the tooltip like I was touching off the part not the tool. Currently I have been storing all tool heights too p59 as a work around.

This seems like a weird way of being setup rather then storing it too it's own unique tool height reference for a tool setter. 

I'd be curious too see how the tool setter macros work exactly where do they store the height of the tool setter 

Maybe this is somthing super basic I have never had to setup a tool setter at work before and as far as I fan tell and when manually setting tool lengths mazak seems to base them on a unique height offset.

Thanks for any and all responses!