Soft Limits and G-Code coordinates

Howdy,
I have all my homes setup up to be the zero's of all of the axis on the global coordinates (table coordinates).. And I have set all of my Soft-limits to the furthest travel (with room for error) my machine can handle.. So X is 0" to 50", Y is 0" to 27" and Z is -7.5" to 0" (with home being at zero).

This works great jogging around and not crashing.. However if I my work coordinates and try to run a program it says that it can't because the program is outside of the soft limits.. For instance if I try to run the sample, because Z rises to .12 for a few rapid movements, even if I am globally at -3, but the G54 coordinate is zeroed it still says its out of range..

How can I configure Linux CNC to use the soft limits globally (track where the machine is/moving in the table cooridnates) but let G-Code file coordinates (like say g54) do their own thing... For instance, if I zero Z (for G54) at -3" from the Home switch.. Then I should be able to run G-code that moves the machine up to +3" (ish) as that is the actual limit.. I shouldn't be blocked by +.5" as being above the soft limit as the soft limit should only be in consideration from the perspective of the table, not the G-Code coordinate.

Anyways, Thanks in advance.

Ok, so the Touch Off button is different then zeroing the coordinate systems... This is a machine I am setting up for a local High School so I am coming from Mach 3/4.. Used to just zeroing and though the touch-off button was going to run a probe command..

Thanks, It will be this weekend before I can test again ( funny how work is right on top of when schools are open lol)...