There are 3rd party applications that some people use with Mach3. Search online and the forums at MachSupport.com for more.
The only probing we support is the G31 straight probe (http://machmotion.com/cnc-info/g-code.html#G31_Straight_Probe). Wiring the touch probe would be similar to wiring up a limit switch. You can wire the touch probe to one of the inputs on the Apollo board and then in the Mach3 software (config=>ports&pins=>input signals) you can enable the probe input and set the port and pin for the input you wired into.