A couple of things to consider before just going ahead with your optimization efforts.
1: If you have two css style sheets that are in different folders but are used for different things and are called the same EG folder1/style.css folder2/style.css Google will rename them to style and style_2 so beware of this so you do not overwrite the wrong files.
2: Google will let you download all files but only into 1 folder so you have to find where each file resides correctly.
3: As always when you optimize content ensure you take a backup and rename your files to .old before overwriting just to be sure.
I like the way google are really pushing forward with making the web a better, faster place.