apm2.6 compass motor calibration help!

I finally tuned my quad with the apm2.6 board with version 3.1.2
But when I fly in loiter mode my quad tends to do the toilet bowl dance. This I because the magnetic north changes because of the magnetic interference caused by all the electronics onboard.
The solution to this is to do compassmot stated in the 3dr website. What this does is tells the compass the correct north by not registering the magnetic interference.

But I don’t know that whether should I power my APM board with battery and USB at the same time or not. The Jp1 jumper is plugged in the board.
I need some assistance regarding this.
Should I remove the jumper and then power with USB and battery or what? :confused:

Yes you need to plug in the USB and battery at the same time. I have my jumper installed and have gone through the sequence of compassion which fixed my toilet bowling in loiter

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now one more problem has come up.
after the compassmot my interference was 5%, but now my motors are not spinning fast enough to take off even on highest throttle.