There is no one size fits all of where to position the Spindle in your mount on your Z-Axis and several considerations need to be taken into consideration. 

Considerations include:

• Length of your longest / shortest bit
• Height of your normally tallest stock
• Desire to cut through with your shortest bit
• Reach of any sort of tool setter
• Overall clearance of the Z Plate

A typical rule of thumb is install the shortest bit and bring your z down to the lowest position and tighten your mount down. Then install your tallest bit, and jog your Z all the way up, and compare that to the position of your bottom Z plate / your tallest anticipated stock. 

Because of the numerous variables with wasteboard height, Z travel, bit length, stock thickness we can't say "this is where you should put it." Being a cylindrical body, you can place it at any height but would not recommend at either extreme of the top/bottom. 

With ATC, and the use of the Flush Racks, which are included, the easiest solution is to jog your Z all the way down and rest the spindle on the waste board without a tool holder in the cone.

With either the qcw, short, or tall tool racks this might cause lost available travel, and in which case refer to the above listed guidance.