"When I started learning about godarays I also assumed that the sun had to be above or indside the cloud layer,but upon further experimentation I find it does not."

Actually the sun is above the clouds. Always:-) Well, almost always - if you point the sun upwards it will be below the clouds, which could lead to some "interesting" effects....

The sun is an infinite-type light, and as such the only thing that matters is the direction it's pointing. You can place an infinite light anywhere in a Vue scene (I've never tried placing one below ground, but even that should work).

Hope that helps,

Cheers,
Diolma