In Mach the
M05 // Turn off spindle
G00 X0.0000 Y0.0000 Z2.0000 // go to (0,0,2)
M06 Txx // Tool change
M03 // Start spindle
where xx is a different tool number will tell Mach to pause (unless the user has changed the default setting that is). Can't speak exactly for EMC as I was never able to get it to run on my laptop.
Jay