Not sure what you mean by default .htm file. The pages are php based and are based off of a template. The templates that the pages are based on are located in the Templates directory.
The css files are located in the css and CSSMenuWriter directories.
Not sure what you mean by skin or entry file.
For your extensions install, I would recommend installing one and then testing it out and getting familiar with it before installing the next. Since there are so many extensions, getting to understand them individually first would be helpful to being successful with the extensions.
