The CssLink server control resides on the master page while CssRegistration controls may be placed on a master page, page layout, or content page.
When the page is assembled, all of the style sheets are rendered by the CssLink control. The CssLink control renders registered style sheet links in alphabetical order, then Core.css is rendered, finally themes are registered. If the styles that you define in your .css file are also in Core.css or the theme they will be overwritten (typical .css behavior).