Settings Home Location is a different thing.
I haven't used Basic+Mag+GPS. I always use INS13. I always use AuxMagSettings.Usage=AuxOnly. Don't forget to calibrate your mags.
Those AuxMag instructions are long winded, but it is important to read and understand, otherwise you are as bad off as a cave man that I throw my car keys to and tell him to go get a hamburger.
Well almost...
(note that I just pushed a source code change (25 May 2016) that makes the following numbers correct again)
GPSV9 and DJI GPS/mags both start with BoardRotation=0,0,0
Most PixHawk GPS/mags start with BoardRotation=0,180,0 (180,0,180 also works. Prove it by flipping your hand around.)
These are ALL numbers you start with. If you have race tilt motors that are tilted 15 degrees, you must subtract 15 from Attitude->Settings->RotateVirtual->Pitch (so usually -15) and you must add 15 to AuxMagSettings.BoardRotation.Pitch (so 195 for many PixHawk GPS/mags).
If you don't have race tilt motors, you leave those numbers alone.
Think of a single dice (a western right handed dice) that must be glued on in the correct orientation. "One" must be pointing forward. But that isn't enough. Two must be pointing right and three must be pointing down. (If your dice is left handed, 3 will be pointing up and there is nothing you can do about it.)
The 3D (forward-backward, right-left, down-up) (forward, right, and down are all positive direction) mag sensor just tells what it sees. Example: For me in North America where north is also 62 degrees down if I point the quad nose north and 62 degrees down, the FC should see +400 on the forward-backward (x) mag sensor. If the sensor is installed incorrectly (same thing as BoardRotation set wrong), it may see +400 on the left and right mag sensor. will get confused and the HUD will wobble roll and flip around constantly (INS13 at least).
BoardRotation MUST be set correctly. If you have your PixHawk GPS/mag installed pointing forward, that is usually pitch=180 (or roll=180, pitch=0, and yaw=180 also works).
The instructions posted are a way of determining whether you have BoardRotation set correctly. My BoardRotation is set correctly and I am in North America where north is north and also about 62 degrees down. If I point my quad nose at north I get about +400 on x (and small values on y and z). If I flip the quad to point the tail at north then I get -400 on x (and still small values on y and z). Repeat for y and right side. Repeat for z and down. This tells me that BoardOrientation is correct. Set your AuxMagSettings.BoardRotation.Pitch to 180. Look up your magnetic inclination (dip) on the following map. Verify that your x, y, and z now look correct.
https://upload.wikimedia.org/wikipedia/commons/d/de/World_Magnetic_Inclination_2015.pdfFor northern hemisphere north is also downward. For southern hemisphere north is also upward. Don't worry, it is just the magnetic field direction.
My main test quad uses INS13 with a 30 back degree tilted FC/PixHawkGPS/mag stack that simulates 30 degree race tilt motors.