The way that CSS works, if any style declarations override previous style declarations, only the most recent declaration is used. For example, if I had a stylesheet that had the following code in it:.wrapper {margin:10px;}
.wrapper {margin:0;}
The wrapper class would have a margin of 0, since that was the last declaration to be read by the rendering engine. So, in your case, if you want to override the functionality of the gantry.css file, you can just add the appropriate style declarations to any of the CSS files that are loaded after gantry.css.
The second issue you're having sounds like a permission problem. Make sure that the user or group that your webserver is running as has the necessary permissions to make changes inside your base path and recursively throughout all of the enclosed directories.