trying to better understand tool length offsets, electronic tool length sensor

i have been building my machine for quite a while now, and still have no real idea of the whole procedure for setting offsets. keep in mind, i am a carpenter, thus my woodworking CNC router table, so precision machine setup is rather foreign to me.
A bit of machine background for those that do not know me. it is a Techno/ISEL 4-foot by 4-foot (rough working area) machine, that i have fitted an ATC spindle to in prep for building a linear tool rack. i have an electronic tool length sensor, but no material-top touch sensor yet. i do have a 3D probe, though.
so, my setup process so far has been a little weak. after homing, i just load in the tool i will be using, move the machine rapidly to the rough material origin, and then slowly align the tool visually to the origin, and for Z, i place a piece of paper down and slowly lower the Z until the paper no longer moves. then i set X,Y,Z zero.
so, being in the configuration category, my desire to understand is so i can develop some G-code macros to automate the process faster.
i have the toolchanger macro mostly done, though i need to actually build the rack to verify it. It includes calling a macro to check the tool lengths after change, though it is commented out for testing, as it probes, but I don’t think it does so correctly.
For reference, my entire running configs are at: github.com/travis-farmer/linuxcnc

my idea of a better setup system, with no idea of correctness: to start with, I would like the tool db to have correct tool lengths, as my ATC spindle is fairly repeatable, I think (BT-30, ISO-30 ATC tool holder system). So I want a macro that I can call to update a tool in the tool DB, or at least provide the tool length number that I can enter into the tool DB. That way, when I change tools, I don’t need to check offsets every time with the tool length sensor.With that in mind:
step 1) I would like to probe the material height, zero Z
step 2) then change to tool #1 (a sharp pointed carbide, for cheap PCB engraving)
step 3) use point to align X and Y over the material origin, zero X, Y
step 4) remove tool #1
step 5) run program (includes picking up tools as needed, and using the tool db for length/diameter)

so if I store tool lengths in the tool db, how do I go about getting the numbers to enter, using the 3D probe that I get material Z zero with as the reference?
It all seems awkward to me, as the tool sensor is table mounted, and Z origin is at the top most point of Z travel. but this also seems safest for homing.
My gantry slides are mounted under the table, so if the table sags with age, and I hope it does not, the gantry will follow it. So it is my understanding that Z-origin is a fixed point above the table.

Hmmm, perhaps wrong forum. feel free to move to forum.linuxcnc.org/40-subroutines-and-ngcgui if it would be better suited.

ok, my understanding for getting a reference point, would be to probe the table with the 3D probe. while it is still at the trigger point, use my calipers to measure to the spindle nose, a fixed target. use that number to subtract from the 3D probed material height and set to work Z zero.
or i could measure to the tool-holder ISO-30 fork ring as my fixed point. i don't want to measure to the collet nose as it can change with torque.
but anyway, if all my tools are measured from the lowest point to the ISO-30 fork ring, then when a tool is loaded from the tool DB, wont LinuxCNC add the tool length to this point, and have the tool offsets correct?
but i would have to probe and set an offset for the probe, correct? so if in the macro, i probe down, pause at probed point so i can set work zero. and if the probe is a numbered tool, like #99, i can set the length of the probe in the tool DB.

then, for measuring in tool length, i could either hand-measure with my calipers, or with the tool length sensor.
my thinking on that, is if i probe the table to get my distance from the Z zero to table, add the 3D probe length, and store it. then i probe a tool, and measure from the table to the top of my tool sensor to get the sensor height when probed. i subtract the tool sensor height from the Z zero to table height. this gives me a value that when i probe a tool, i can subtract the probed value from it, and get the tool length to store in the tool DB.
seems complicated, but that is just to get the values to adjust the probed length from. i can have the macro just spit out the number for me, and i can add it to the tool DB myself.

of course, this all depends on how accurate my digital calipers are.

ok, assuming the above idea works... how to i check for tool wear after selecting a tool and compensate for it? i guess G43.2 is involved, but i am unsure how...

This may help.
Measure the probe. I make this tool 99. Its best to do this setup on the milling table with the probe powered so you can see exactly at what height it is when triggered. My Probe is Tool 99
 

Just measure your tools the same way. I number them from 01 and up

 

Enter the lengths into the tool table on the machine
I select tool 99, insert the probe, probe to the workpiece surface (when I locate the origin of the machining job, usually top left corner for me cos thats what I always used on a manual mill)

So then as tools change, linuxcnc will account for the difference in length between the probe and the tool.