In my case, I created a share extension (jar) where I put my css overrides:
\my-extension-share\src\resources\META-INF\themes\myTheme\presentation.css
\my-extension-share\src\resources\META-INF\themes\myTheme\yui\assets\skin.css
so that when jarring the extension project, the files are under
\META-INF\themes\myTheme\presentation.css
\META-INF\themes\myTheme\yui\assets\skin.css
within the jar.
Deploy the jar to <Alfresco>/tomcat/webapps/share/WEB-INF/lib