Your Z-Offset is burned into the memory of the printer from the factory. If significant maintenance or a replacement extruder has been made you may be required to modify the Z-Offset.
From MatterControl 1.7 onwards you have the ability to change the Z-Offset while printing using a process called "babystepping". Babystepping adjusts the software Z offset and the values are added or subtracted from the firmware offset. Typically the offset may be changed by up to 0.3mm to get optimium results, this is especially helpful when setting up a new printer. Here is a great detailed article on how to use babystepping
To adjust the offset burned into firmware
See this related article