You don't add any css to the css files except custom.css. Otherwise you'll run into issues.
For what you are trying to do, I disagree with Nick and it would be incredibly cumbersome to remove everything with css. You would be much better off just finding an html template with a slideshow and using that. Then linking to that page outside of wordpress.
For the menu question, I don't know what you mean. If you put css in a file, and pull in that file correctly to a page then the css will take effect.
If it isn't then either the css or the html is incorrect.