Sure. There is a button in the addon's preferences. Note, it will replace all buit-in presets with new copies, so any save changes to them will be lost. Your own custom presets won't be affected though and will still exist.

Yes, it uses the world shader and will cast ambient light in combination with a sun or moon light.

Yes, you do whatever you like so long as its within the base level node tree. There is also a 'Base' colour input which can be used to mix in an image texture.

Not any more. 0.2.1 removes the need to have the addon installed with the exception of animating the shadow caster size.

There's a good chance you have enabled the sun position addon. This will override any manual changes you make to the sun position to one calculated by time and latitude/longitude. To manually control the Sun, simply disable the addon in preferences>Add-ons 'Sun Position'.

PSS to Panorma

Position camera to X0,Y0,Z0, rotate X90d.

Set render engine to Cycles and change camera type to Equirectangular.

Output resolution should be 2:1 ratio ie. 2048x1024

Hit render and save!

Panorama to Cube Map

You can use this website to genreate png or jpeg cubemaps from your equirectangular texture.

https://jaxry.github.io/panorama-to-cubemap/

Yes, pressing Ctrl-H will reveal the clouds mask socket.