Hi ,
I think I can see some of the confusion.
Ok usually the REF ALL AXIS HOME for x and y is 0,0 and in the lower left corner (machine coordinate with home switches). When you go y4 it will move to y +4. If you then go y2 it will move y2, all of these numbers are positive. you would have to to go y-4 to get in to - numbers, but if your home is 0,0 then you couldn't physically move past your home position witch should be the physical limits of your machine. Now all of this is assuming you have home limit switches installed and properly configured.
else { you don't have any home switches and you are using the zero buttons to set a home position, then depending on how you generate your gcode will dictate where the 0,0,0 position is relative to the 0,0,0 on your part. in this case things could go to - based on how your part g code was made.
OR you do have home switches installed and you are setting a offset relative to the machine coordinate.
This is kind of a confusing aspect of cnc work. The best thing to do is go to the WWW.mcahsupport.com site and look at the coordinate systems video, then the homing and offsets video. It took me a couple of times through the videos and a lot of experimenting to get my head around it.
Chad
Oh yea and usually the Z 0 at the up most position, and negative into the work.
Just thought of something else in case you aren't thoroughly confused yet. There are settings for Incremental and absolute positioning. I would recommend looking this up in the mach manual. It will probably do a better job of explaining it than I would.