I have a Bridgeport Boss 6 that I retrofitted but I don't know how to set up the e-stop so that if I use the one on the machine it will stop everything. The way it is right now if I use the machine e-stop the spindle stops but the bed still is working off of the mach 3. It is dangerous that way and I would like to change it to where using the machine e-stop will stop everything. I hope I can get some help on how to wire it. A diagram would be helpful.

That all depends what your estop is doing now.

if you can attach another set of contacts or you have a spare pair then run a wire from ground to one side and another from the second side to an input on your bob and tell mach that that input is e-stop

If the e-stop is used on the machine the spindle stops but the things controlled by Mach3 keeps working (the x,y, z) If I use the e-stop on the mach3 the steppers all quit but the spindle keep turning on the machine. I am accustomed to using the e-stop on the machine so all the movements keep working but the spindle stops. Very dangerous.

Look at the EStop switch on your machine - if it has a spare (unused) set of contacts then connect them as Graham has suggested. If there is not a spare set of contacts, could you fit a new microswitch which is operated by your machine EStop switch ?  then connect that switch as Graham has suggested.

Tweakie.

I am including the electrical diagram of the machine

So your ES is switching off some kind of "main" power supply, but your diagram is incomplete
Some more of the diagram is needed where is seen where your spindle is connected.

What I am trying to do is make the breakout board's E-stop mach3 by using the The E-stop in the diagram. Mach 3 is what is running my steppers motion and the machine's e-stop doesn't trigger the E-stop in Mach3 I just want the e-stop on the machine to trigger an e-stop in mach3. That would then in turn stop everything.

Take a picture of the contacts on the estop on the machine and post it here

You could add a relay with its coil connected to wire 128 and wire 2. It will be energized when the E-stop switch is in the run position. The diagram doesn't tell what the control voltage is but you can measure the voltage out of the transformer. Use a normally closed contact from that relay to extend the E-stop to mach3.
If you are using servo motors consider using another contact to disconnect the power to them to ensure they can't runaway due to an internal fault.
If you run hazardous voltage from one enclosure to another add a notice so people won't assume opening the local disconnect makes the area safe to work in.

Thanks MN300 I am pretty sure I will need a relay. I need to check it out but I think the voltage is 24 volts from the E-stop on the machine. I am using a cheap breakout board and the pin used on it is pin 10. I am sorry I can't explain any better but electrical work is not one of my strong suits, On the relay I would like to figure out how to get it to either turn both machine and breakout board e-stops on or off at the same time. I really need a diagram if someone can post one. Thanks all for the help you are trying to give me. I am pretty sure that the breakout board will be of a different voltage than the breakout board. When I posted this I thought I might connect with someone that has retrofitted a Bridgeport boss 6. The mach 3 is only running my motion of X,Y,Z