In the manual, you will find a whole section on that topic.
With most products the manual goes in the trash with the wrapping, however with a shopbot, you will really want to know it.
Search for the section with the big title:
Temporary Zero Points When Cutting Files
In the users manual (in my copy it is on page 19). That is what that section is all about. Of course you could just use K and move to a new point on the material, set Z2, and run the cut file again. Sometimes I do that, but the master file method is much more repeatable, and you can MIX which parts you want to cut, it does not have to be just one part. You can make seven of the first part and four of some other part all in the same operation. (Presuming you dont have to change bits.)
With a little experience you will be able to use the same technique even with manual bit changes.
Hope that helps-
D
"The best thing about building something new is either you succeed or learn something. Its a win-win situation."
--Greg Westbrook