It's just a standard setup. Look at any original easystar config.
Get it setup, and your regular RC working right, and then put the APM in the loop. After a radio config, you should be good to go.
I typically put it on the aileron channel. That way up/down, left/right is all on the right stick on Mode 2 transmitters.
Throttle only on the left.
yes, the rudder servo should go on channel 4. You then should setup a KFF_RDDRMIX of 1 to mix the rudder in from your roll control. After that you can tune your RLL2SRV_* PIDs normally.
I have now tried all PID setups and I'm not able to make the rudder move when the plane is rotated around its z-axis (yaw). The rudder moves only when the plane banks and I don't think that is how it is meant to work.
that is actually normal for FBWA and STABILIZE modes. In those modes the plane is not trying to hold a heading - the heading is controlled by the pilot banking the plane. It only tries to hold a heading in AUTO, GUIDED, RTL or LOITER modes where it has a navigation target. In those modes it will try to turn towards the right heading. That turn involves banking the plane over (using the rudder in your case) and then using the bank angle to change heading. That is the normal way a plane flies.
As I mentioned earlier, you should set KFF_RDDRMIX to 1. Leave the RLL2SRV_* values as the default.
Planes fly by inducing roll, either with aileron or rudder, and using that to turn. Turning by directly yawing the plane is very inefficient, and is generally considered to be bad flying. If the plane had passengers they would likely need their airsick bags :-)