The autoload directory is to add your custom css files, not for overriding existing css.
But for css, that's usually what you want. Add your css rules that have higher priority, so browser will use it.
For example, if the css rule you want to change look like this:
.sf-menu {
float: left;
margin-bottom: 1em;
}
and you want to change margin-bottom, you can create css file that contains only change:
.sf-menu {
margin-bottom: 2em !important;
}
Browser will use all rules and merge them together. Because of !important keyword, the your custom value for margin will be used.
So -- do not copy the original file, but only copy rules you want to change.