Yes thats correct for machine coords. You can however have positive Z moves in your work offsets though. For work offsets the top of thge stock is normally zero so an inch above is +1 and an inch below is -1.
If it works fine on the machine then look in the Mach3 folder and copy the xml for the profile you use and then paste it into the Mach3 folder of your desktop computer. If you are using the standard mill profile the file you are looking for is Mach3Mill.xml
Hood