Should I be running the calibration with or without stock?

Should I be running the calibration process with or without stock? For instance, I’ll primarily be cutting ¾ plywood, would it be slightly more accurate if I calibrate with that thickness on top of my wasteboard?

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It generally shouldn’t matter, but to get maximum precision you want to enter the thickness of the wood in the settings here:

That way the internal math can compensate for it.