Yes. MatterControl and most 3D printing software expects dimensions to be given in millimeters. If you made your design using some other unit of measurement then you will need to scale your model appropriately. You can do this in MatterControl using the Scale menu in Edit mode. It has a built in list of factors for scaling between common units.
The TAZ 6 does automatic leveling by probing the corners of the bed. You'll have to change the Z offset through the printer's menu. If you are adding a 3 mm plate, then you would add 3 mm to the Z offset.