When I home my xy coordinates don't go to zero, I have the green check mark for auto zero checked in the homing tab.  Any suggestions?  Thanks

Press the machine CoOrds button, they should be at zero, you are probably looking at your Work CoOrds.
Hood

I'm pretty Green, Thanks

Your machine displays two forms of DRO. One is Machine Co-ordinates the other is Program Co-ordinates.

Machine Co-ordinates are the machines own reference by which it regulates all it's movements. This is displayed when the machine co-ordinates button is pressed (red surround is lit). It can only be zeroed by the "RefAllHome" button. If you press this button, your machine should visit the three "home" switches and stop there, and zero all it's references. It now knows where it is.

It is unlikely that this position will be much good for general machining work and will certainly not be the place from which most of your GCode programs start - which on a mill is usually (although not always) at the bottom left hand corner of the workpiece, with the cutter resting on the top of the workpiece.

If you zero your machine co-ordinates then change your display to program co-ordinates, by pressing the machine co-ordinates button so the light goes out, you can zero this display (if not already at zero) by typing in zero at each one.If you then jog your machine to it's working position - say - where the program starts, and then note the display - this is the offset from your machine co-ordinate zero. If you now zero this DRO's again, the program will run from this new position. (but if you check machine co-ordinates, it still has these in it's memory)

If you now look at your offsets - in Config/Fixtures - you will see that G54 now has the offsets that you just noted entered into it.
G54 is the default offset. You also have g55 to g58 and g59p7 to g59p255 (I think) - anyway, plenty to go at.

If you are a professional machine shop, then, then first thing that happens in the morning is that the machines are zero'd - i.e. all are set "RefAllHome". The fixtures table is filled in with offsets for all the various programs, and so the program will start with say - G56,G0X0Y0. The machine will then pick out the offset for G56, and move to the new 0.0 position ready to start work.

You don't necesarily need to work with offsets - but if your are wiring up your home switches, I would think you will