I'm using a 57E Pokeys and an M16 BOB. For the limit switches I understand that Pokeys now supports limits being used for home limits as well. On the board there are X, Y, Z and A inputs for wiring the limits. Obviously daisy chain two together per axis.

But what I need to know is one wire goes to the pin for the axis, but where does the other wire go to the "GND" pin or the "5V' pin? Thanks.

GND

This didn't work. When I use the 5V it does.

yer it goes from limit pin to ground

When the limit switches, being NC, are not triggered does the Pokeys 57E board have red LEDs by the limit RJ45 Port? I ask because when I had GND hooked up to the limit switches common wires the LEDs were barely lit up. I mean hard to even see. When I use 5V they light up bright. When I push on a limit switch to simulate a trigger the LED turns off.

I'm not sure if this is normal or not, but I'm also having another weird problem. The E-Stop button is NC, normally closed, but I have to have the checkmark box for 'invert estop' check marked to have it work. It's totally backwards. I wonder if there's something wrong with my board.

PoKeys devices use active-low state for the inputs (all have pull-up resistors). So, switches and other sensors must be connected in such a way that they make a contact between the input and the GND.

I think the board I had was bad. I've since returned it.

The pull-up resistors, are they built into the pokeys or do I have to add them?

Weak pull-up resistors are already built-in. If longer wires are used to connect signals to PoKeys device, additional external pull-ups (1 kOhm) are suggested.
If internal pulse generator is used, there is a requirement for 470 Ohm pull-up resistors on step signal pins (see the manual on Pulse engine and Mach3).