I have a delta printer. I modified my marlin to allow me to use the same pin I use for my Z_max as also my z_probe pin. It seems to work fine but my problem is that when calibrating, when the probe hits the bed the endstop also activated and it stops my autocalibration. Making it stop checking for endstops when calibrating should fix this problem but I can't seem to narrow down where that code is. I've been checking on the marlin_main.cpp. Thanks in advance.

Not sure why you have Z_Max as your Probe Pin since the Z Probe for a delta should be on the Min Endstop.
But to disable/enable software endstops, in configuration.h set these lines as shown:

#if ENABLED(MIN_SOFTWARE_ENDSTOPS) || ENABLED(MAX_SOFTWARE_ENDSTOPS)
  #define SOFT_ENDSTOPS_MENU_ITEM  // Enable/Disable software endstops from the LCD: You'll need this enabled when setting Z-Probe Offsets 
#endif

This will put a menu item under Prepare -> Move Axis (after doing Prepare -> Auto Home) called 'Software Endstops' that will allow you to enable/disable them.
Then you can (carefully) move the z axis below zero to adjust bed height.

Hope this helps.