skin.css that comes with the skin you are using is the place to put your styles into. There are three levels of CSS in DNN - default, portal and skin (also containter and module) in addition to normal hierarchy of styles - external, page and inline. DNN doesn't have any special rules for styles to be applied, but if you are not careful with the hierarchy of these styles... your changes are not going to work.

The answer is all of the above. You can re-upload your skin (dangerous, though - you may excidentally overwrite some other changes you had...), you can FTP the CSS file - it's in /Portals/Skins/whateverthenameofyourskin... (or, possibly, in a futher subfolder) or, if you uploaded your skin under Host, it's in _default/Skins/whatever..., and, finally, you can redefine styles in portal.css as this file get's loaded last (after default.css and skin.css)