Yes.
If you have Mach3 configure to "Stop Spindle, Wait for Cycle Start", it will run the M6Start, then wait for you to hit Cycle Start. After Cycle Start, it will run the M6End, then continue with the g-code.
If you configure Mach3 for Auto Toolchanger, then it will only run the M6Start macro, then continue running the g-code.