I'll let Joe D help with the css but here is some info that will help you.
Any css files in your skin folder that are not listed in the style.config file can be safely deleted. stylelayout.css is not used anymore and it can be deleted as can styleborders.css, stylecolors.css, styleimages.css which are now all combined in style.css. I probably should have told you to delete all the skins from /Data/Sites/1/skins before copying them, then you would not have the extra legacy files.
There are other files that are used though, consult the style.config file to know what is safe to delete.
The files listed in style.config are combined together according to their sequence in the style.config file and minified. So you can actually organize your css into as many or as few files as you want according to your own preferences, and you can make some skins share files froma common location as well.
For more info on style.config see this page
Hope it helps,