Generally I don’t try to shove every tool path into 1 gcode file.
I break up the post process by bit size.
In Fusion CAM side, just select the tool paths with the same size bit and for the post file select the MPCNC_Fusion360.cps
To rezero you can move the z down until the new bit barley touches the surface and issue a G92 Z0 manual command in Repetier-Host.
If you look at the sample gcode I posted, at the very top there is a G92 X0 Y0 Z0 – that sets the xyz axis to zero where the bit is currently at.