It's all spelled out in the Installation Manual in pretty good detail, but there are some level checks that have to be done, then you have to "swing" the compass in the GMU 11 (it walks you through it on-screen).
As @bradg33 noted, it's all spelled out in the manual... but the main steps are level plane and calibrate the pitch/roll offsets, then do the vibration test. You'll then need to do the GMU calibration, this should be done in an area as free of obstacles and such as possible (you'll want to be away from big steel buildings, areas of taxiways that might have steel plates for access to underground utilities, etc). The calibration essentially involves turning the aircraft in 15 degree increments, guided by the G5. You then want to do a compass swing to verify the GMU is accurate in its headings. A compass rose is generally a great place to do the initial calibration as they are generally away from anything that could create magnetic disturbances, and then you can do the swing right after to validate the calibration. The magnetometer interference study should have been done prior to the mounting of the magnetometer, but it's not a bad idea to double check.