There are several steps which are a bit involved to explain here. The best bet is to go through the entire setup. The AP-11 manual is online at Simrad's website. The main changes you will need to make during the procedure are:
o calibrate the rudder
o swing the compass (slow circle to find magnetic deviations)
o calibrate the compass heading (I use GPS while moving in several directions to average out the best reading)
o zero the rudder (ensure the boat moves straight when the rudder feedback is at zero)