I've just updated our article Creating Skins from Artisteer Templates. It was confusing because Artisteer used to call the project type "Html", but in version 3 they now call that project type or export type "Website or Blog".
If you follow the instructions and start with the correct existing skin as a starting point you should not have to modify theme.skin and layout.master should also have most if not everything correct already, though it is possible that it may need some minor tweaks if it doesn't work right away, you can compare the markup from layout.master to the outer html in the exported index.html file.
The only reason to modify style.config is if you wanted to include additional css file(s).
It is possible that you will need to tweak the style-artisteeroverides.css and or other css files since Artisteer doesn't produce CSS for every mojoPortal feature.
You should never modify the style.css file which is exported from Artisteer nor any of the files exported from Artisteer, all overrides should be in other files so it is always safe to tweak the design in Artisteer and re-export it.
Hope that helps,