As far as fixture offsets are concerned, I mount a travel indicator in the spindle, zero it on the table, and record the number in Z from the screen. Then, zero the indicator on top of the part and record the Z value. (make sure you use the same zero on the indicator). on my machine, the first value is negative, so what I do is disregard the negative sign and add the 2 numbers together as positives. the result is your Z fixture offset. I also set all my tools from the same spot on the table as where I zero the indicator, so there is less room for error. hope this helps.
No, really, just my .002"