Toolsetter configuration

I'm trying to figure out the best way to set up my toolsetter. Right now I'm just using it semi-manually, in that I first reference the empty spindle, then I reference a tool, and manually subtract the values to get the tool length, then enter that into the tool table.

I currently reference the work using a Haimer 3D Taster, whose length is set as tool 98.

My homing switches are "better than 0.001"" repeatable, which is not as good as I would like, but probably the best that can be expected from this rack-and-pinion gantry table (AvidCNC). I think I can determine the location of the top of the toolsetter in machine coordinates, and then I should be able to touch off tools after homing the machine without the intermediary step of referencing the spindle.

But I'm a little unsure of what should be in the tool table. I guess it doesn't really matter, so long as all the tools are measured with respect to the Haimer, right?