My home position is head all the way up with the spindle centre over the back right hand corner of the envelope.
I have Home Offsets programmed into Mach3 which then set my zero at X & Y centres of movement with my standard edge finder touching the table surface (with it's tool offset selected), this way when you Ref All Home Mach3 goes and finds the home switches then applies your Home Offsets.
Then you have multiple Work Offsets which allow stored settings for all 3 axes for clamps, vices, fixtures, standard workpieces etc.
Then you have Tool Offsets which allow stored settings for the lengths of the various standard tools you use.

Once you've got your head around it all set-ups become far faster and simpler, Ref All Home the machine, select the tool of your choice and the work offset of your choice and your zero can be where you want it in little more time than it takes to fit the tool and position a vice on the bed,

- Nick