LinuxCNC logo pattern - Z axis initial condition, writing, and retraction ??

I am using the LInux CNC emblem program to demo my mill. I have some initial condtion and operation questions.
1. I am running the program 'dry', that is away from the bed.
2. First I homed the Z axis. (as well as X and Y)
3. I then started the program.
The Z axis went to minus about -.078 for writing. The retractions went to about .1.
My questions are:
1. Why would the 'writing' position go negative, that is below the zero postion.
2. If I were to actually use a sharpie to write the emblem how can I adjust the parameters so the sharpie meets the paper with the proper tension.
Thanks Dan

Generally you set Z = 0 to be the top of the work. This is the easy surface to probe / touch-off.

So it it usual for all cuts to be in negative Z.

There are other ways to do it, it's up to you. But the logo code expects the top of the work to be the G54 Z=0.