CSS alone won't work. Anything you do in CSS will happen after the image has already been resized and hence will stretch/squish the image hence why you've GOT to do it in JS.
There is a good discussion of it in the comments of the JS library this plugin uses: http://buildinternet.com/2011/07/supersized-3-2-fullscreen-jquery-slideshow/
search for the word "offset" and modify according your needs. Maybe someday someone will update the JS library to take a top/right/bottom/left offset or padding value... currently it doesn't.
For example for my site I subtracted 75 here:
// Gather browser size
var browserwidth = base.$el.width(),
browserheight = (base.$el.height()-75),
and elsewhere added 75 to center:
// Vertically Center
$(this).css('top', ((browserheight - $(this).height())/2)+75);
You could then save this modfied script in your theme, deregister the script that the plugin uses and register your own in it's place (I haven't gotten to that part yet, but that's the best way I can think of to handle it all).