I'm assuming you are referring to the minimum software endstops. You would not want to override the minimum hardware endstops since that would mean parts crashing into each other. The minimum software endstops are handled in the firmware, so if you want to disable them, you can do that in your Configuration.h file. You also have the option of tricking the firmware to think you are at a different position than you really are. So if you do a movement to Z=0 (i.e. "G1 Z0 F8000") and then you tell the firmware that position is actually Z=5 ("G92 Z5"), that will allow you to move even lower.
There's a reason the software endstops are there though! As you mentioned, you need to be extremely careful doing this as you can easily crash hardware into itself.