Go slow

I'm a noob to the fun stuff.
I have worked on the machine about a year and a half. Currently all we do is load up a customer drawing of a pcb into gc-prevue. I get the xy coordinates and write the program for our machine manually. I have been wanting to make carvings out of wood for a while but never knew how. I have been searching and came accross this site.
Should I look on the machines control system to see if I can change where the z zero is? When you refer to setting it up for your stock do you change it all the time depending on what size material you are trying to cut?
I am trying to make a cut out of a chevy emblem for starters. I load the bmp into the mesh software, but when I look at the code it spits out, it is all neg z's. If I were to put this code into our machine it'd either error out in the z axis or try to drive the head through the table.