Thanks, found them. I removed the lines from init() and wrote in my template to load just the layout css.
I am wondering why SS puts the code always at the end of the <header> element. Even I put it in my template above other meta tags.
Will's suggestion is the best, but if it's too difficult to refactor your CSS, the only thing I can think of is to remove the SS specific inclusions and hard code the <link> tags in the template where-ever you want them to appear.
You do lose SS's cool versioning/cache system however.
It's a pity. That does make things more complicated (as stated above) and isn't quite like the other flexible "you-have-the-control" thing of SS.
Can you think of a nicer way to provide the order? Perhaps an array which defines the order.... Sometimes providing a massive set of configuration options throughout the core is more trouble than using the other workarounds. After using SS for quite a while I've don't think I have ever needed to configure the order of the requirements.