Be extremely cautions if you set your tools with the "Auto Set" button as it will automatically subtract any value you have set in User Parameter > Switch 1 > Number 7. This value is typically set to the height of your tool setter (table to trigger height).
If you record this number and save it somewhere, then make it zero or whatever size gage block stack you are using, it will automatically subtract that value from the machine position. So say you're using a 4.000" gage block and touching tools to the table, like you would with a tool setter, put 4.000" in that location and it will automatically subtract it for you if you press Auto Set while in the tool length offset field.
You'll need to repopulate the tool height value back in there when the tool setter is replaced, but it should be calibrated and most likely will result in a new value anyways.