think there is a couple of solutions, you will need to pick the one that fits
so machine home is the location of the machine home, where the 0 is on each physical axes. this let the machine know where the limits are. then there a work spaces this let you move where 0 is in relation to your program, then there is tool comp this defines where the tool is after you turn it on.
the machine should be homed before you load your parts there should be a switch that it "home" to every time you turn the software off, if the machine crashes, or you other wise lose your position.
then you need to touch off, i use a fixed point like a corner or a probe.
this moves the G-codes work space the actual numbers you wrote.
now you can touch off your tool, this will give you the length in relation to the work space zero. when you call a tool then do a cutter comp turn on move it will adjust for the tool length and you will get the right cut. if you don't shutoff or crash the machine, you can put the next part in and touch off and go.