So, I have two 2.5 boards one for a plane, one for a regular helicopter.
One has a gps with the magenetometer on the gps board, and the other is going to be with a straight gps.
Since it may be nice to consider moving them back and forth, which would only involve a jump solder to fix, (but that can be problematic) or do I want to commit one board to the external compass?
Are these magnetometer’s on a separate board superior to the ones on the main board?
As far as I know the magnetometers are the same type, the separation is what improves the performance.
You want to use a separate magnetometer in order to be able to place it where you will not get interference.
The magnetometers are very subject to electro magnetic interference, commonly caused DC by battery, power distribution board and ESC’s and AC by motors and board electronics themselves.
It is actually better to be several inches away from batteries, power distribution and ESCs since they produce a large electromagnetic field which varies according to power being used.
And the highly variable AC / DC fields of the motors can also have a considerable influence.
Since the flight controller is very often placed at the worst possible point relating to these influences it is often necessary or at least very desirable to move the magnetometer to a location outside the EMF areas of influence.
Fixed DC influences can generally be compensated for (in firmware) so long as they don’t “saturate” the magnetometer, but since most of these are related to current power consumption they are generally highly variable and cannot be accounted for.
In your case it might be best to try it first with internal magnetometers on both frames and then see which one is worst and use an external mag.
Of course if they are both bad, the solution is to get another external mag board.