I have followed the instructions on http://code.google.com/p/arducopter/wiki/AC2_Magnetos for adding the Magnometer directly to the APM board in the components down pins forward orientation. I have the APM board mounted according to http://code.google.com/p/arducopter/wiki/AC2_Frame_Assembly where the RC pins are towards the back of ArduCopter and which places the Magnometer on the "front". I have an X configuration with the APM pointed between the 2 legs.
I noticed in the Mission Planner that the HUD shows the ArduCopter pointing S when it's really pointing north. Moving the ArduCopter shows the heading changing the correct amount but always off by 180 degrees. I guess what I am doing is looking to confirm that I actually have assembled things correctly. For reference I am using https://store.diydrones.com/ProductDetails.asp?ProductCode=BR-HMC58....
I would appreciate any suggestions on what I may have done incorrectly.
I don't see anything other than the RC receiver on the tray above it and all of the Oilpan, etc parts that it is mounted over. I did some additional readings outside. The "Actual" column is provided by my Iphone in "True North" mode, while the reading column is what was displayed in the HUD in the APM Planner.
Thanks for your replies. I thought about it some more and decided to go ahead and move the RC receiver from the top shelf to the same shelf as the PDB. That resolved the problem I was having with the magnometer! Everything seems to be in order now. Thanks again to everyone for their help.