Ok, the tool length offset table

I have no ATC

I'm going to try R8 ER collet chucks or the Torch TTS system as a repeatable method of tool holding, have asked many people and resounding reply was yes it should be plenty accurate enough for this style of machine, so....
1 - With the tool offsets, can I measure them using the Z axis probing and touch-plate setup?
2 - I guess i need a "default zero tool" or some-such to enable a reference length to be kept and then I would measure all tools against that one? This would be tool zero or 250 etc?
3 - If i was using the tapping head say, i would need to lower the knee about 5", ref the surface again, tap the threads then return the knee roughly to the higher position. Fit the next tool, set the tool number in Mach3, ref the surface and good to go again??
Am i on the right tracks here?