My recommendation is don't try to change things in the core of mojoportal. If you do that you are forking the code and it will be difficult for you to get upgrades and bug fixes in the future. Of course nothing forces you to follow my advice but you can't expect support from me if you change the architecture.
Better to leave the core css files in the root of the skin folder. If you want to include additional stylesheets you can use @import, see inside the style.css for example syntax.