The tool change position is where you want the tool to move so you can change it.
The fixed plate is a plate mounted fpr the automatic auto zero.
When you get to an M6, then the M6 macros are running, so you can't run the other macro. To work like you want to do, you'd need to change the M6 macros to do the regular auto zero during a tool change.
It wuold be easier to just use separate programs for each tool, so you could zero in between.
But it's far simpler to mount a fixed auto zero plate on your machine, and let Mach3 do all the work for you, automatically.