The markup other than what you put in the layout.master is generated by the cms so the layout.master is the only place where you can use custom arbitrary css class names. So for most things you need to use the existing css class names.
So the process is start with a copy of an existing skin and edit styles for existing class names. View the source of the page in the browser as needed to find the markup you are trying to style and find what class names you can use.
Its not going to work by just including some arbitrary css file with arbitrary class names and selectors.
Hope it helps,