APs and systems are entertaining (evil laugh) because they have so much stuff to change. and every time you tweak a parameter on either it will likely need adjustment to the other.
But again,
This is what I suggest you begin doing
1. Install the FGDATA next with submodules, and use SHIFT+F4 there to reload autopilots on the fly, or patch your fgdata yourself
http://wiki.flightgear.org/Howto:Design ... ation_file2. Start following the wiki page above with a flying plane. Basically activate the autopilot roll mode, and start altering the code with small jumps (by 1 or 2 at a time, up and or down) see if it improves, and or worsens (SHIFT F4 to reload the stepwise change). When you see that it goes worse instead of better, half the step size (example do 0.5 increase/decrease if you were doing 1), and repeat. Until you fell that a change of 2 steps (the smaller size you get) does not change your behavior anymore, and you achieve parameters that give you stable flight.
3. Move to other modes of AP.
If you want a more complete autopilot to begin with (I totally suggest that), try installing either Josh's IT or JWocky's SYS8 as a first step.
That's how I go about finding a good parameter number-set for a given plane (assuming the FDM was good already)
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If you cant' fly a plane by hand, the FDM is totally messed up and there's no point to edit APs at that stage yet. Get the FDM adjusted is step one, everytime.