Yes - pin 5 is normally at 5v for normal running. If it is taken to 0v then it shuts down the drive. If a fault occurs on the drive, it goes to 0v.
The problem is Mach 3 has no "two way" pins - i.e. those that work as inputs and outputs. So therefore you must wire all three Geckos together so that they shut each other down - with a lead , via a diode, to the input pin of Mach3, to tell the computer.
The problem is, is you have Mach 3 shutting down the drives, then it will also put a 0v signal into the input to Mach 3 telling it there is a fault - and, therefore, you will need some complicated logic to sort out the timing of the signals.
Let the Geckos look after themselves, I think.
As far as the 5v reset signal is concerned, the easiest way is to drive a small relay from one of the output pins - and have this put a 5v signal into the Gecko. This can be software driven from your reset button - or perhaps cycle start button - on a Macro. It can be timed to put a 5 sec pulse, or whatever is required. At the end of the pulse, you can check the "fault" input pin and see if it has reset,(it will, whilst the 5v from the relay is present, not show a fault, but revert to 0v if there is still a fault on the Geckos) and then return.