Are you talking about a taig mill with CNC done by the factory? or by an aftermarket conversion company? or a do-it-yourself CNC conversion? The answer could be different for each of them.
The "home position" (the position the mill goes to after the switches are tripped) doesn't really matter. I set mine so the spindle is clear and the table is in a position where doing setups is easy.
The best position of the switches themselves depends on if you have position feedback on your axes. For steppers with no feedback, you want the switches near the end of travel of an axis such that the initial position when the home command is given is always on the same side of the switch. Which way the axis moves (positive or negative) doesn't really matter as long as the home switch is tripped before you hit a mechanical stop. For the Z axis, it makes sense to put the switch at the upper limit of spindle travel, but for the X and Y axes, the end of travel where the limit switch trips doesn't really matter.
You might also consider installing home switches on both sides of the travel and switching between them every few months. This would tend to distribute wear on the screw more evenly over time, and might possibly minimize excessive backlash from developing in one area of the screw travel. This is also a good reason to do setups for jobs across the table, not just setting up on the same end over and over again.