I think we got a bit pushed off you post - so - The way the switches are programmed varies, whether the computer is using them as limit switches or homing switches.
As a limit switch, the carriage hits the switch, opens it, and the machine stops dead, and the reset button starts to flash. We never did get you over your problems with this - so
Your problem is that, when you hit the RESET button to start again, the limit switch is still open, so immediately triggers the STOP again.
If you go to the Settings Page (Page 5) left hand column, Special Functions, you will see the Auto Limits Overide button. If you press that, the machine will allow you to back off the switch if you hit it.
A further problem is noisy switches - that is where the movement of the switch is so jerky, that it doesn't make a clean on/off contact, but stutters. Mach 3 is so fast, it can pick up this, and although the switches closes, if it opens again a fraction of a second later, Mach sees this as the Limit switch being hit again, and stops the machine.
To counteract this, go to Config/General Config and on the top right hand corner, increase the debounce to say 50 units - a bit on the top side, but you can reduce it later when you get set up.
This should set up your Limit Switches. A word, though - these switches are what they say - LIMITS of the system - and your machine should not hit them. As Hood has said, elsewhere I think - you can set soft limits on your machine so that the machine will not hit the limit switches - which are there to stop it to prevent a major catastrophy - not just an emergency.
When the same switches are used as a home switch, the operation is different. The carriage hits the switch and opens it, stops, reverses until the switch closes again, then stops. In theory this is more accurate than just hitting the switch, because the speed at which the machine backs off can be controlled. Mine are accurate to less than one thou (although I use lasers instead of mechanical switches).
If on your Config/Homing you have Auto Zero ticked, the Machine Co-ordinate DROs will go to zero.
Again the same problem with noisy switches may occur, so debounce is even more important here.
This sets up your Machine Co-ordinates - your machine knows where it is, and controls its movement using these - but they are probably *** all use from a prgrammers point of view. For this you need to place your cutting tool at the 0,0,0 point of the program you are cutting, so that (as in your other post) the entire cut is within the parameters of your table. This can take some doing if it is a big cut on a small table.
If you come out of Machine Co-ordinates and go to Program Co-ordinates - this now equates to your program Place the cutter where your 0.0.0 position is and press the zero button beside each DRO - they will go to zero
If you check Machine Co-ordinates you will see that has not changed, and if you check in Config/Fixtures, you will see that G54 has in the set of figures shown on your Machine Co-ordinates. This is the offset the machine requires to convert your program co-ordinates to machines co-ordinates for it to cut in the correct place. There are about 255 offsets available in the offset table - and so when you get really going, each program can have its own offset, so the machine always runs from the same, correct starting place.
Hope this helps explain a bit and starts you thinking why your machine is doing what it is doing.
The is a video tutorial worth looking at - Co-ordinate systems - which will help explain it and may make the above a bit more transparent.