hi,
My problem is when I do the compass-motor calibration the total mag field interference is shown 36%. I am not using any apm power module. so I measure compass vs. throttle. Thus that could be problem when I fly in auto mode? I don’t have any other place to mount the apm. 
what Should I do?
I would suggest that you mount the APM board on some carbon fiber plate (make sure the board does not touch directly) as the CF plate usually does a decent job at blocking interference. Otherwise try to move your ESC as far from APM as possible.