Regards rge machine Zero, you need Auto Zero checked on the Homing and Limits page. If your Home position is not with the tool fully negative in X and Y and fully positive in Z then Home off values would be needed.
Hood

Done! now I have all axis' enabled and homed but "A" (slaved to "X") on pin 12 and X, Y, and Z on pin 13 on the inputs signals screen. Now how do I set up home so when "machine coord's" is lit, to display machine 0,0? In other words, how do I set up homing correctly now that my inputs are correct and motors are running correctly? 

Regards rge machine Zero, you need Auto Zero checked on the Homing and Limits page. If your Home position is not with the tool fully negative in X and Y and fully positive in Z then Home off values would be needed.
Hood

I want home position to be when X and Y are fully neg but when I travel to the switches, which are set to X,Y, and A home neg, the machine does not show 0,0. All are already set t Auto Zero by default and I have not changed them.

Are you definitely looking at machine coords?
If so please attach your xml and I will simulate here and see if i can find the issue.
Hood

The machine coord light is on and I it is not at 0,0. If I have the correct setting, and I trip the switch which is set to home and auto zero, shouldn't it auto zero on the DRO?

Its working fine here in simulation so not sure whats wrong. Try disabling the A Axis home and limits and see if that helps for the time being.
What I did was simulated your Home switches, pressed ref all and Z starts moving up and I sim the switch it backs off stops and sets the machine coords DRO to zero then Y then X.
Justin case, r Machine coords is when button has red showing round it.
Hood

No, it works, I clicked on ref all home and it did work great! I didnt know thats the button to use because it screwed up the tracking when I didnt have "A" set on its own pin. I get t now.

thanks Hood, if it weren't for you I would be hanging from a bridge..........