Mixing minified and non-minified files

In my website I have a mix of minified and non-minified js and css files.

Does this plugin detect if a file is already minified and leave it as it is before mergin? Or can I manually specify which files to minify and merge?

I am asking since I also have W3 Total Cache installed and when I set the minification to auto, my site broke.

Thanks in advance.