My technique for god rays. .... if it helps ...
A couple of points first:
You won't get god rays if the sun is behind the camera.
You wont see god rays if the sun if fully illuminating where the camera is.
Firstly turn off the atmosphere node and any high cirrus clouds.
Make a copy of the render camera and plug this into your render node. keep the old camera, you'll need this for your final render.
Using the "Navigation Controls" (the compass like control in the top right of the 3d preview, point the camera towards the sun.
Allow your 3d preview to fully render and hit pause. You'll see white clouds against a black sky.
Go to object preview mode so you can see the cross hairs of the sun and move it till it's just behind a cloud. Where the camera is should be in shadow, the area where the god rays illuminate should be in front of the camera. If needed change the coverage and seed of the cloud.
Once the sun/cloud/camera are in the right position you can re-enable the atmosphere and other clouds and you should see god rays.
Go back to your original camera to check and hit render.
Repeat this process until you get something you like.
If your using TG3 you can render out an Atmosphere Direct pass which can be used to enhance the god rays (increase it's contrast) and layer it in additive. Check Digitalguru's render layers for details.
Hope this helps
Richard