It depends on the option you have set in General Config.
You can have one of three options.
1. Ignore Toolchange
2. Stop spindle and wait for cycle Start
3. Auto Tool changer
First one does exactly what it says, it just continues and wont do anything
Second on will stop the spindle, apply the offsets and wait for you to swap your tool then you press Start and it continues.
Third is as it says, it is for an automatic toolchanger and it will look at the M6Start.m1s macro to see what has to be done, this obviously is customised to your turret.
So if you have a manual tool change then option 2 is what you want, if you have an automatic turret then option 3 is what you want.
One thing to be careful with option 2 is that your profile has not been cloned from a mill profile as a Mill uses the M6End.m1s macro and that will move your axes after you press Start. So if using option 2 have a look at the M6End macro and make sure it doesnt have any code in it.
Hood