I set all my tool heights from the same position. We have a 50mm high setting gauge that we use, but you can use anything you want. A slip gauge or parallel with a bit of paper for feel. Set your tool against your setting tool, go to tool offset page and hit tool height measure button. Then move your tool up to your work piece, the G54 z dimension is the difference from your tool setting position to the top of your work piece (or wherever you want to set your g54 z zero from). If you material is above your tool set position g54 z will be a positive number and vice versa if material is below setting position.
I keep one tool holder set up with a piece of steel left in it that is set to my tool height gauge setter. This means that tool is a known height so I use that for setting my g54 z zero dimensions, so it doesn't matter how often I change tools over in other holders, as long as I set them to the same tool setting gauge they will jump straight into a program without any issues on height.
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