@mr_z : I should be the last person in the world telling you about design (considering i suck at it and it takes me way to long to do) but like anything else you need to start with a set of blueprints. You cant build a bridge without a plan can you? Even if it is drawing something on paper or using something free like MS Paint, whatever Macs equal is, Gimp, photoshop(30 day trial), etc. When you have all those things down, it gives you a better visual of where you want to begin.
This may or may not help, but something i used to do a long while back when trying to understand why people did what they did, i would go “inspect element” and just add either a 1px border or some inset box shadow around every element to see how it worked.
For example, lets look at CSS-TRICKS (awesomeness!)
Now add a small border with:
* {
border:1px solid red;
}
Now you can simply highlight over every element and see exactly why it is positioned there and you have a more defined look of the sites ‘skeleton’. I hope that made sense and possibly helped you with your design ideas.